Hello !
When I want import T1 MRI Bias Corrected using the General Import function, it doesn't work.
Please find below the error message.
Is there a bug ?
Thank you.
Marine
Traitement Importation générale 1 démarré sur 2009/11/26 10:55
dans Importation de données 65 Impossible de convertir la donnée d'entrée
RuntimeError
neuroProcesses.py (1811) in _processExecution:
result = process.execution( self )
ImportData.py (90) in execution:
raise RuntimeError( _t_('Cannot convert input data') )
dans Importation générale 1 Impossible de convertir la donnée d'entrée
RuntimeError
neuroProcesses.py (1811) in _processExecution:
result = process.execution( self )
GeneralImport.py (104) in execution:
context.runProcess(importer, input=self.input.fullPath(), output=self.output)
neuroProcesses.py (1656) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1811) in _processExecution:
result = process.execution( self )
ImportData.py (90) in execution:
raise RuntimeError( _t_('Cannot convert input data') )
Traitement Importation générale 1 terminé sur 2009/11/26 10:55 (0 seconds)
general import error
Re: general import error
Finally, I have to, first import the corrected MRI (using another software) as T1 Raw MRI into BrainVISA, and second import this corrected MRI in BrainVISA as T1 MRI Bias Corrected always into BrainVISA.
Perhaps these details could help you to understand what happened.
Marine
Perhaps these details could help you to understand what happened.
Marine
-
riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
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Re: general import error
Hi Marine,
This error message means that no conversion process was found to convert input data to the output format. Which formats have you used (both for input and output) ?
Thus I don't understand why the T1 importation worked and the generic import failed...
Denis
This error message means that no conversion process was found to convert input data to the output format. Which formats have you used (both for input and output) ?
Thus I don't understand why the T1 importation worked and the generic import failed...
Denis
-
riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: general import error
Hm, you're right actually, there was a bug here... the converter query (almost) always failed. I wonder if it is a new bug or if it always existed...
I have fixed it on our repository, it will be part of the next update.
In the mean time you may convert the input data to the right format first (using the AimsConverter process, int tools/converters), or AimsFileConvert command by hand, then use the import process. Not very convenient, but it will be fixed...
Denis
I have fixed it on our repository, it will be part of the next update.
In the mean time you may convert the input data to the right format first (using the AimsConverter process, int tools/converters), or AimsFileConvert command by hand, then use the import process. Not very convenient, but it will be fixed...
Denis
Import error ARRRRRRRRRRRRRRH!!!
Denis,
I use AimsFileConvert to convert DICOM to NIFTI. Since the last version (cartopack-Fedora-4-i686-3.2.0-2009_11_05), AimsFileConvert couldn't recognize DICOM input (AimsFileConvert: ../blablabla/i3703459.MRDC.1 : unsupported data type Volume / UNKNOWN). echo $DCMDICTPATH works. On my computer, the right release for converting DICOM to NIFTI is "cartopack-Fedora-4-i686-3.1.6-2009_05_14".
Best regards
Sebastian
I use AimsFileConvert to convert DICOM to NIFTI. Since the last version (cartopack-Fedora-4-i686-3.2.0-2009_11_05), AimsFileConvert couldn't recognize DICOM input (AimsFileConvert: ../blablabla/i3703459.MRDC.1 : unsupported data type Volume / UNKNOWN). echo $DCMDICTPATH works. On my computer, the right release for converting DICOM to NIFTI is "cartopack-Fedora-4-i686-3.1.6-2009_05_14".
Best regards
Sebastian
Re: general import error
Denis,
interesting command line informations from the two versions of brainvisa :
Brainvisa : cartopack-Fedora-4-i686-3.2.0-2009_11_05
AimsFileInfo --info | grep DICOM
DICOM input : no
Brainvisa : cartopack-Fedora-4-i686-3.1.6-2009_05_14
AimsFileConvert --info | grep DICOM
DICOM input : no
2 DICOM reading
Data type: CartoVolume/DOUBLE - formats : DICOM GIS MINC NIFTI1 SPM
Data type: CartoVolume/FLOAT - formats : DICOM ECAT GIS MINC NIFTI1 SPM VIDA
Data type: CartoVolume/LONG - formats : DICOM GIS MINC SPM
Data type: CartoVolume/S16 - formats : DICOM ECAT GENESIS GIS MINC NIFTI1 SPM VIDA
Data type: CartoVolume/S32 - formats : DICOM GIS MINC NIFTI1 SPM
etc.
Best regards
Sebastian
interesting command line informations from the two versions of brainvisa :
Brainvisa : cartopack-Fedora-4-i686-3.2.0-2009_11_05
AimsFileInfo --info | grep DICOM
DICOM input : no
Brainvisa : cartopack-Fedora-4-i686-3.1.6-2009_05_14
AimsFileConvert --info | grep DICOM
DICOM input : no
2 DICOM reading
Data type: CartoVolume/DOUBLE - formats : DICOM GIS MINC NIFTI1 SPM
Data type: CartoVolume/FLOAT - formats : DICOM ECAT GIS MINC NIFTI1 SPM VIDA
Data type: CartoVolume/LONG - formats : DICOM GIS MINC SPM
Data type: CartoVolume/S16 - formats : DICOM ECAT GENESIS GIS MINC NIFTI1 SPM VIDA
Data type: CartoVolume/S32 - formats : DICOM GIS MINC NIFTI1 SPM
etc.
Best regards
Sebastian
-
riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: general import error
Hi Sebastian,
From the mesages you report, it seem that the dicom plugin isn't loaded (and same for others).
If I run the same command from a 3.2.0 pack on a Fedora 11 system, I get:
Quite a larger list... Now the question is: why do many (maybe all) plugins don't load...
Can you please try re-running the command with "--verbose 2" argument ?
This means that libaimsdicom.so.3.2.0 (with 3 digits) doesn't load, which is normal for now, this behaviour is for future releases, but libaimsdicom.so.3.2 (with 2 digits) actually works.
Now you say it, I have seen recently a Ubuntu system (Yann's laptop, actually) which had strange library paths problems: plugin libraries could not be found, even if they were to be found first in the LD_LIBRARY_PATH list. I had to un-set this LD_LIBRARY_PATH variable before re-running programs of the pack, then it worked. I have never seen this beheviour before, I wonder if it's a "new feature" in recent linux distribs, a mechanism which has priority on the LD_LIBRARY_PATH order or something when loading plugins, or a Ubuntu bug, or... I don't know.
Which system are you running ?
Denis
From the mesages you report, it seem that the dicom plugin isn't loaded (and same for others).
If I run the same command from a 3.2.0 pack on a Fedora 11 system, I get:
Code: Select all
./cartopack-Fedora-4-i686-3.2.0-2009_11_05/bin/AimsFileInfo --info | fgrep DICOM
DICOM input : no
2 DICOM IO
Data type: CartoVolume/DOUBLE - formats : DICOM FDF GIS MINC NIFTI1 SPM TIFF
Data type: CartoVolume/FLOAT - formats : DICOM ECAT FDF GIS MINC NIFTI1 SPM TIFF VIDA
Data type: CartoVolume/LONG - formats : DICOM GIS MINC SPM
Data type: CartoVolume/S16 - formats : BMP DICOM ECAT FDF GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: CartoVolume/S32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/S8 - formats : BMP DICOM GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: CartoVolume/U16 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U8 - formats : BMP DICOM FDF GIF GIS JPEG JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/ULONG - formats : DICOM GIS MINC SPM
Data type: Volume/DOUBLE - formats : DICOM FDF GIS MINC NIFTI1 SPM TIFF
Data type: Volume/FLOAT - formats : DICOM ECAT FDF GIS MINC NIFTI1 SPM TIFF VIDA
Data type: Volume/LONG - formats : DICOM GIS MINC SPM
Data type: Volume/S16 - formats : BMP DICOM ECAT FDF GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: Volume/S32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/S8 - formats : BMP DICOM GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: Volume/U16 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U8 - formats : BMP DICOM FDF GIF GIS JPEG JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/ULONG - formats : DICOM GIS MINC SPMCan you please try re-running the command with "--verbose 2" argument ?
Code: Select all
./cartopack-Fedora-4-i686-3.2.0-2009_11_05/bin/AimsFileInfo --info --verbose 2
libaimsvida.so.3.2.0: libaimsvida.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsvida.so.3.2 successfully loaded.
libaimsdicom.so.3.2.0: libaimsdicom.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsdicom.so.3.2 successfully loaded.
libaimsecat.so.3.2.0: libaimsecat.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsecat.so.3.2 successfully loaded.
libaimsfdf.so.3.2.0: libaimsfdf.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsfdf.so.3.2 successfully loaded.
libaimsjpeg.so.3.2.0: libaimsjpeg.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsjpeg.so.3.2 successfully loaded.
libaimstiff.so.3.2.0: libaimstiff.so.3.2.0: cannot open shared object file: No such file or directory
library libaimstiff.so.3.2 successfully loaded.
libaimsqtformats.so.3.2.0: libaimsqtformats.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsqtformats.so.3.2 successfully loaded.
libaimsminc.so.3.2.0: libaimsminc.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsminc.so.3.2 successfully loaded.
libaimsply.so.3.2.0: libaimsply.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsply.so.3.2 successfully loaded.
libaimsnifti.so.3.2.0: libaimsnifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsnifti.so.3.2 successfully loaded.
libaimsgifti.so.3.2.0: libaimsgifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsgifti.so.3.2 successfully loaded.
libconnectomist_aims_plugin.so.3.2.0: libconnectomist_aims_plugin.so.3.2.0: cannot open shared object file: No such file or directory
library libconnectomist_aims_plugin.so.3.2 successfully loaded.
CartoBase version : 3.2.0
AIMS version : 3.2.0
General information:
global shared path : /home/appli/cartopack-Fedora-4-i686-3.2.0-2009_11_05/bin/../share
aims shared path : /home/appli/cartopack-Fedora-4-i686-3.2.0-2009_11_05/bin/../share/aims-3.2
mmap path : /tmp
nomenclature path : /home/appli/cartopack-Fedora-4-i686-3.2.0-2009_11_05/bin/../share/shfj-3.2/nomenclature
...Now you say it, I have seen recently a Ubuntu system (Yann's laptop, actually) which had strange library paths problems: plugin libraries could not be found, even if they were to be found first in the LD_LIBRARY_PATH list. I had to un-set this LD_LIBRARY_PATH variable before re-running programs of the pack, then it worked. I have never seen this beheviour before, I wonder if it's a "new feature" in recent linux distribs, a mechanism which has priority on the LD_LIBRARY_PATH order or something when loading plugins, or a Ubuntu bug, or... I don't know.
Which system are you running ?
Denis
Re: general import error
Denis,
exactly, the 2 digits dicom plugin fails :
AimsFileInfo --info --verbose 2
libaimsvida.so.3.2.0: libaimsvida.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsvida.so.3.2 successfully loaded.
libaimsdicom.so.3.2.0: libaimsdicom.so.3.2.0: cannot open shared object file: No such file or directory
libaimsdicom.so.3.2: /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/lib/libaimsdicom.so.3.2: cannot restore segment prot after reloc: Permission denied
libaimsecat.so.3.2.0: libaimsecat.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsecat.so.3.2 successfully loaded.
libaimsfdf.so.3.2.0: libaimsfdf.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsfdf.so.3.2 successfully loaded.
libaimsjpeg.so.3.2.0: libaimsjpeg.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsjpeg.so.3.2 successfully loaded.
libaimstiff.so.3.2.0: libaimstiff.so.3.2.0: cannot open shared object file: No such file or directory
library libaimstiff.so.3.2 successfully loaded.
libaimsqtformats.so.3.2.0: libaimsqtformats.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsqtformats.so.3.2 successfully loaded.
libaimsminc.so.3.2.0: libaimsminc.so.3.2.0: cannot open shared object file: No such file or directory
libaimsminc.so.3.2: /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/lib/libaimsminc.so.3.2: cannot restore segment prot after reloc: Permission denied
libaimsply.so.3.2.0: libaimsply.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsply.so.3.2 successfully loaded.
libaimsnifti.so.3.2.0: libaimsnifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsnifti.so.3.2 successfully loaded.
libaimsgifti.so.3.2.0: libaimsgifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsgifti.so.3.2 successfully loaded.
libconnectomist_aims_plugin.so.3.2.0: libconnectomist_aims_plugin.so.3.2.0: cannot open shared object file: No such file or directory
library libconnectomist_aims_plugin.so.3.2 successfully loaded.
CartoBase version : 3.2.0
AIMS version : 3.2.0
General information:
global shared path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share
aims shared path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share/aims-3.2
mmap path : /tmp
nomenclature path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share/shfj-3.2/nomenclature
- Compiled with the following built-in options:
VIDA IO : no
JPEG IO : no
DICOM input : no
ECAT IO : no
Plugin support : yes
Plugins:
0 VIDA IO
1 ECAT IO
2 FDF reading
3 JPEG IO
4 TIFF IO
5 Qt image formats IO
6 NIFTI1 IO
7 PLY IO
8 GIFTI IO
9 CONNECTOMIST IO
- IO types and formats:
Input formats:
Data type: carto_volume of S16 - formats : GIS
Data type: genericobject - formats : PYTHON XML
Output formats:
Data type: carto_volume of S16 - formats : GIS
Data type: genericobject - formats : PYTHON
- AIMS IO types and formats (old API):
Data type: Bucket/DOUBLE - formats : BCK
Data type: Bucket/DTITENSOR - formats : BCK
Data type: Bucket/FIXEDDTMODEL - formats : BCK
Data type: Bucket/FLOAT - formats : BCK
Data type: Bucket/QBALLMODEL - formats : BCK
Data type: Bucket/S16 - formats : BCK
Data type: Bucket/VOID - formats : BCK
Data type: CartoVolume/CDOUBLE - formats : GIS TIFF
Data type: CartoVolume/CFLOAT - formats : GIS TIFF
Data type: CartoVolume/DOUBLE - formats : FDF GIS NIFTI1 SPM TIFF
Data type: CartoVolume/FLOAT - formats : ECAT FDF GIS NIFTI1 SPM TIFF VIDA
Data type: CartoVolume/LONG - formats : GIS SPM
Data type: CartoVolume/POINT3DF - formats : GIS
Data type: CartoVolume/RGB - formats : BMP GIF GIS JPEG JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: CartoVolume/RGBA - formats : BMP GIF GIS JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: CartoVolume/S16 - formats : BMP ECAT FDF GENESIS GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: CartoVolume/S32 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/S8 - formats : BMP GENESIS GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: CartoVolume/U16 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U32 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U8 - formats : BMP FDF GIF GIS JPEG JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/ULONG - formats : GIS SPM
Data type: CartoVolume/VECTOR_OF_3_S16 - formats : GIS
Data type: CartoVolume/VECTOR_OF_6_FLOAT - formats : GIS
Data type: Graph/VOID - formats : ARG BUNDLES GraphVolume
Data type: Hierarchy/VOID - formats : HIE
Data type: Mesh/VOID - formats : GIFTI MESH PLY POV TRI VRML1
Data type: Mesh4/VOID - formats : MESH PLY POV
Data type: Motion/VOID - formats : TRM
Data type: Segments/VOID - formats : MESH PLY POV
Data type: Texture/FLOAT - formats : GIFTI TEX
Data type: Texture/POINT2DF - formats : GIFTI TEX
Data type: Texture/S16 - formats : GIFTI TEX
Data type: Texture/S32 - formats : GIFTI TEX
Data type: Texture/U32 - formats : GIFTI TEX
Data type: Texture/VECTOR_OF_2_S16 - formats : GIFTI TEX
Data type: Volume/CDOUBLE - formats : GIS TIFF
Data type: Volume/CFLOAT - formats : GIS TIFF
Data type: Volume/DOUBLE - formats : FDF GIS NIFTI1 SPM TIFF
Data type: Volume/FLOAT - formats : ECAT FDF GIS NIFTI1 SPM TIFF VIDA
Data type: Volume/LONG - formats : GIS SPM
Data type: Volume/POINT3DF - formats : GIS
Data type: Volume/RGB - formats : BMP GIF GIS JPEG JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: Volume/RGBA - formats : BMP GIF GIS JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: Volume/S16 - formats : BMP ECAT FDF GENESIS GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: Volume/S32 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/S8 - formats : BMP GENESIS GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: Volume/U16 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U32 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U8 - formats : BMP FDF GIF GIS JPEG JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/ULONG - formats : GIS SPM
Data type: Volume/VECTOR_OF_3_S16 - formats : GIS
Data type: Volume/VECTOR_OF_6_FLOAT - formats : GIS
Data type: VolumeRef/CDOUBLE - formats : ALLVOLUMES
Data type: VolumeRef/CFLOAT - formats : ALLVOLUMES
Data type: VolumeRef/DOUBLE - formats : ALLVOLUMES
Data type: VolumeRef/FLOAT - formats : ALLVOLUMES
Data type: VolumeRef/LONG - formats : ALLVOLUMES
Data type: VolumeRef/POINT3DF - formats : ALLVOLUMES
Data type: VolumeRef/RGB - formats : ALLVOLUMES
Data type: VolumeRef/RGBA - formats : ALLVOLUMES
Data type: VolumeRef/S16 - formats : ALLVOLUMES
Data type: VolumeRef/S32 - formats : ALLVOLUMES
Data type: VolumeRef/S8 - formats : ALLVOLUMES
Data type: VolumeRef/U16 - formats : ALLVOLUMES
Data type: VolumeRef/U32 - formats : ALLVOLUMES
Data type: VolumeRef/U8 - formats : ALLVOLUMES
Data type: VolumeRef/ULONG - formats : ALLVOLUMES
Data type: VolumeRef/VECTOR_OF_3_S16 - formats : ALLVOLUMES
Data type: VolumeRef/VECTOR_OF_6_FLOAT - formats : ALLVOLUMES
Data type: genericobject/any - formats : PYTHON XML
Data type: object/object - formats : PYTHON XML
- Graph sub-formats readers:
Generic
roi
- AIMS settings:
{
'__syntax__' : 'aims_settings',
'spm_input_radio_convention' : 1,
'spm_input_spm2_normalization' : 1,
'spm_output_radio_convention' : 1,
'spm_output_spm2_normalization' : 1,
'spm_output_4d_volumes' : 1,
'nifti_output_4d_volumes' : 1,
'default_writers' : {
'Mesh' : 'MESH',
'Volume' : 'NIFTI1'
}
}
I use x86_64 FC11 (uname -a : Linux saturne 2.6.30.9-96.fc11.x86_64 #1 SMP Wed Nov 4 00:02:04 EST 2009 x86_64 x86_64 x86_64 GNU/Linux).
I find a bug in the previous AimsFileConvert version (may be still present) from DICOM to NIFTI: the output NIFTI is "NEUROLOGICAL" oriented in the corresponding field anyway the orientation is actually RADIOLOGICAL. It's quiet confusing. Using the same binary, the conversion from DICOM to ANALYZE is OK for the orientation field ("RADIOLOGICAL").
Additionaly, if the DICOM images are acquired from TOP to BOTTOM, the Z orientation is wrong after DICOM>NIFTI or DICOM>ANALYZE using AimsFileConvert (tag Sup for BOTTOM).
Best regards
Sebastian
exactly, the 2 digits dicom plugin fails :
AimsFileInfo --info --verbose 2
libaimsvida.so.3.2.0: libaimsvida.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsvida.so.3.2 successfully loaded.
libaimsdicom.so.3.2.0: libaimsdicom.so.3.2.0: cannot open shared object file: No such file or directory
libaimsdicom.so.3.2: /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/lib/libaimsdicom.so.3.2: cannot restore segment prot after reloc: Permission denied
libaimsecat.so.3.2.0: libaimsecat.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsecat.so.3.2 successfully loaded.
libaimsfdf.so.3.2.0: libaimsfdf.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsfdf.so.3.2 successfully loaded.
libaimsjpeg.so.3.2.0: libaimsjpeg.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsjpeg.so.3.2 successfully loaded.
libaimstiff.so.3.2.0: libaimstiff.so.3.2.0: cannot open shared object file: No such file or directory
library libaimstiff.so.3.2 successfully loaded.
libaimsqtformats.so.3.2.0: libaimsqtformats.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsqtformats.so.3.2 successfully loaded.
libaimsminc.so.3.2.0: libaimsminc.so.3.2.0: cannot open shared object file: No such file or directory
libaimsminc.so.3.2: /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/lib/libaimsminc.so.3.2: cannot restore segment prot after reloc: Permission denied
libaimsply.so.3.2.0: libaimsply.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsply.so.3.2 successfully loaded.
libaimsnifti.so.3.2.0: libaimsnifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsnifti.so.3.2 successfully loaded.
libaimsgifti.so.3.2.0: libaimsgifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsgifti.so.3.2 successfully loaded.
libconnectomist_aims_plugin.so.3.2.0: libconnectomist_aims_plugin.so.3.2.0: cannot open shared object file: No such file or directory
library libconnectomist_aims_plugin.so.3.2 successfully loaded.
CartoBase version : 3.2.0
AIMS version : 3.2.0
General information:
global shared path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share
aims shared path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share/aims-3.2
mmap path : /tmp
nomenclature path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share/shfj-3.2/nomenclature
- Compiled with the following built-in options:
VIDA IO : no
JPEG IO : no
DICOM input : no
ECAT IO : no
Plugin support : yes
Plugins:
0 VIDA IO
1 ECAT IO
2 FDF reading
3 JPEG IO
4 TIFF IO
5 Qt image formats IO
6 NIFTI1 IO
7 PLY IO
8 GIFTI IO
9 CONNECTOMIST IO
- IO types and formats:
Input formats:
Data type: carto_volume of S16 - formats : GIS
Data type: genericobject - formats : PYTHON XML
Output formats:
Data type: carto_volume of S16 - formats : GIS
Data type: genericobject - formats : PYTHON
- AIMS IO types and formats (old API):
Data type: Bucket/DOUBLE - formats : BCK
Data type: Bucket/DTITENSOR - formats : BCK
Data type: Bucket/FIXEDDTMODEL - formats : BCK
Data type: Bucket/FLOAT - formats : BCK
Data type: Bucket/QBALLMODEL - formats : BCK
Data type: Bucket/S16 - formats : BCK
Data type: Bucket/VOID - formats : BCK
Data type: CartoVolume/CDOUBLE - formats : GIS TIFF
Data type: CartoVolume/CFLOAT - formats : GIS TIFF
Data type: CartoVolume/DOUBLE - formats : FDF GIS NIFTI1 SPM TIFF
Data type: CartoVolume/FLOAT - formats : ECAT FDF GIS NIFTI1 SPM TIFF VIDA
Data type: CartoVolume/LONG - formats : GIS SPM
Data type: CartoVolume/POINT3DF - formats : GIS
Data type: CartoVolume/RGB - formats : BMP GIF GIS JPEG JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: CartoVolume/RGBA - formats : BMP GIF GIS JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: CartoVolume/S16 - formats : BMP ECAT FDF GENESIS GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: CartoVolume/S32 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/S8 - formats : BMP GENESIS GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: CartoVolume/U16 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U32 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U8 - formats : BMP FDF GIF GIS JPEG JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/ULONG - formats : GIS SPM
Data type: CartoVolume/VECTOR_OF_3_S16 - formats : GIS
Data type: CartoVolume/VECTOR_OF_6_FLOAT - formats : GIS
Data type: Graph/VOID - formats : ARG BUNDLES GraphVolume
Data type: Hierarchy/VOID - formats : HIE
Data type: Mesh/VOID - formats : GIFTI MESH PLY POV TRI VRML1
Data type: Mesh4/VOID - formats : MESH PLY POV
Data type: Motion/VOID - formats : TRM
Data type: Segments/VOID - formats : MESH PLY POV
Data type: Texture/FLOAT - formats : GIFTI TEX
Data type: Texture/POINT2DF - formats : GIFTI TEX
Data type: Texture/S16 - formats : GIFTI TEX
Data type: Texture/S32 - formats : GIFTI TEX
Data type: Texture/U32 - formats : GIFTI TEX
Data type: Texture/VECTOR_OF_2_S16 - formats : GIFTI TEX
Data type: Volume/CDOUBLE - formats : GIS TIFF
Data type: Volume/CFLOAT - formats : GIS TIFF
Data type: Volume/DOUBLE - formats : FDF GIS NIFTI1 SPM TIFF
Data type: Volume/FLOAT - formats : ECAT FDF GIS NIFTI1 SPM TIFF VIDA
Data type: Volume/LONG - formats : GIS SPM
Data type: Volume/POINT3DF - formats : GIS
Data type: Volume/RGB - formats : BMP GIF GIS JPEG JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: Volume/RGBA - formats : BMP GIF GIS JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: Volume/S16 - formats : BMP ECAT FDF GENESIS GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: Volume/S32 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/S8 - formats : BMP GENESIS GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: Volume/U16 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U32 - formats : BMP FDF GIF GIS JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U8 - formats : BMP FDF GIF GIS JPEG JPEG(Qt) MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/ULONG - formats : GIS SPM
Data type: Volume/VECTOR_OF_3_S16 - formats : GIS
Data type: Volume/VECTOR_OF_6_FLOAT - formats : GIS
Data type: VolumeRef/CDOUBLE - formats : ALLVOLUMES
Data type: VolumeRef/CFLOAT - formats : ALLVOLUMES
Data type: VolumeRef/DOUBLE - formats : ALLVOLUMES
Data type: VolumeRef/FLOAT - formats : ALLVOLUMES
Data type: VolumeRef/LONG - formats : ALLVOLUMES
Data type: VolumeRef/POINT3DF - formats : ALLVOLUMES
Data type: VolumeRef/RGB - formats : ALLVOLUMES
Data type: VolumeRef/RGBA - formats : ALLVOLUMES
Data type: VolumeRef/S16 - formats : ALLVOLUMES
Data type: VolumeRef/S32 - formats : ALLVOLUMES
Data type: VolumeRef/S8 - formats : ALLVOLUMES
Data type: VolumeRef/U16 - formats : ALLVOLUMES
Data type: VolumeRef/U32 - formats : ALLVOLUMES
Data type: VolumeRef/U8 - formats : ALLVOLUMES
Data type: VolumeRef/ULONG - formats : ALLVOLUMES
Data type: VolumeRef/VECTOR_OF_3_S16 - formats : ALLVOLUMES
Data type: VolumeRef/VECTOR_OF_6_FLOAT - formats : ALLVOLUMES
Data type: genericobject/any - formats : PYTHON XML
Data type: object/object - formats : PYTHON XML
- Graph sub-formats readers:
Generic
roi
- AIMS settings:
{
'__syntax__' : 'aims_settings',
'spm_input_radio_convention' : 1,
'spm_input_spm2_normalization' : 1,
'spm_output_radio_convention' : 1,
'spm_output_spm2_normalization' : 1,
'spm_output_4d_volumes' : 1,
'nifti_output_4d_volumes' : 1,
'default_writers' : {
'Mesh' : 'MESH',
'Volume' : 'NIFTI1'
}
}
I use x86_64 FC11 (uname -a : Linux saturne 2.6.30.9-96.fc11.x86_64 #1 SMP Wed Nov 4 00:02:04 EST 2009 x86_64 x86_64 x86_64 GNU/Linux).
I find a bug in the previous AimsFileConvert version (may be still present) from DICOM to NIFTI: the output NIFTI is "NEUROLOGICAL" oriented in the corresponding field anyway the orientation is actually RADIOLOGICAL. It's quiet confusing. Using the same binary, the conversion from DICOM to ANALYZE is OK for the orientation field ("RADIOLOGICAL").
Additionaly, if the DICOM images are acquired from TOP to BOTTOM, the Z orientation is wrong after DICOM>NIFTI or DICOM>ANALYZE using AimsFileConvert (tag Sup for BOTTOM).
Best regards
Sebastian
-
riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: general import error
Whew, an error message I've never seen !libaimsdicom.so.3.2: /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/lib/libaimsdicom.so.3.2: cannot restore segment prot after reloc: Permission denied
After googling your error message, it seems that it is SElinux which doesn't allow plugins to load (why this one and not all of them ? I have no idea...)
Look for instance at the first answers in google: http://www.appistry.com/community/forum ... ion-denied, or http://www.archiware.com/support/index. ... ticleid=58.
However the third one, http://www.quantumwise.com/forum/index.php?topic=16.0 seems to suggest a cleaner solution, less radical than just switching SElinux off.
Please tell us if one of these works...
Denis
-
riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: general import error
For the second part of your message,
The Dicom reader in Aims is clearly incomplete and had a lack of maintainance for years, and I am not really surprised that it doesn't handle orientation correctly (it probably doesn't take care of it at all). Fabrice has recently made some changes and improvements in it, as well as added writing support for Dicom. But I don't know if such an orientation problem is fixed or not. Moreover it doesn't really explain why Analyze and Nifti formats behave differently... or maybe yes after all but I'm not sure right now before investigating further.
I just hope you will be able to run the 3.2 version to test this and report again if it still fails, because orientation problems are always incredibly complex to track and I don't want to get a headache if the problem has been fixed since then...
Denis
(I guess it's better to start a new topic for a different problem, but never mind)I find a bug in the previous AimsFileConvert version (may be still present) from DICOM to NIFTI: the output NIFTI is "NEUROLOGICAL" oriented in the corresponding field anyway the orientation is actually RADIOLOGICAL. It's quiet confusing. Using the same binary, the conversion from DICOM to ANALYZE is OK for the orientation field ("RADIOLOGICAL").
Additionaly, if the DICOM images are acquired from TOP to BOTTOM, the Z orientation is wrong after DICOM>NIFTI or DICOM>ANALYZE using AimsFileConvert (tag Sup for BOTTOM)
The Dicom reader in Aims is clearly incomplete and had a lack of maintainance for years, and I am not really surprised that it doesn't handle orientation correctly (it probably doesn't take care of it at all). Fabrice has recently made some changes and improvements in it, as well as added writing support for Dicom. But I don't know if such an orientation problem is fixed or not. Moreover it doesn't really explain why Analyze and Nifti formats behave differently... or maybe yes after all but I'm not sure right now before investigating further.
I just hope you will be able to run the 3.2 version to test this and report again if it still fails, because orientation problems are always incredibly complex to track and I don't want to get a headache if the problem has been fixed since then...
Denis
Re: general import error
Denis,
I try the third method. I use, as root, "chcon -t texrel_shlib_t /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/lib/*". The dicom conversion is OK.
Here the output of AimsFileInfo --info -verbose 2
libaimsvida.so.3.2.0: libaimsvida.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsvida.so.3.2 successfully loaded.
libaimsdicom.so.3.2.0: libaimsdicom.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsdicom.so.3.2 successfully loaded.
libaimsecat.so.3.2.0: libaimsecat.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsecat.so.3.2 successfully loaded.
libaimsfdf.so.3.2.0: libaimsfdf.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsfdf.so.3.2 successfully loaded.
libaimsjpeg.so.3.2.0: libaimsjpeg.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsjpeg.so.3.2 successfully loaded.
libaimstiff.so.3.2.0: libaimstiff.so.3.2.0: cannot open shared object file: No such file or directory
library libaimstiff.so.3.2 successfully loaded.
libaimsqtformats.so.3.2.0: libaimsqtformats.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsqtformats.so.3.2 successfully loaded.
libaimsminc.so.3.2.0: libaimsminc.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsminc.so.3.2 successfully loaded.
libaimsply.so.3.2.0: libaimsply.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsply.so.3.2 successfully loaded.
libaimsnifti.so.3.2.0: libaimsnifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsnifti.so.3.2 successfully loaded.
libaimsgifti.so.3.2.0: libaimsgifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsgifti.so.3.2 successfully loaded.
libconnectomist_aims_plugin.so.3.2.0: libconnectomist_aims_plugin.so.3.2.0: cannot open shared object file: No such file or directory
library libconnectomist_aims_plugin.so.3.2 successfully loaded.
CartoBase version : 3.2.0
AIMS version : 3.2.0
General information:
global shared path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share
aims shared path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share/aims-3.2
mmap path : /tmp
nomenclature path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share/shfj-3.2/nomenclature
- Compiled with the following built-in options:
VIDA IO : no
JPEG IO : no
DICOM input : no
ECAT IO : no
Plugin support : yes
Plugins:
0 VIDA IO
1 ECAT IO
2 DICOM IO
3 FDF reading
4 JPEG IO
5 TIFF IO
6 Qt image formats IO
7 MINC IO
8 PLY IO
9 NIFTI1 IO
10 GIFTI IO
11 CONNECTOMIST IO
- IO types and formats:
Input formats:
Data type: carto_volume of S16 - formats : GIS
Data type: genericobject - formats : PYTHON XML
Output formats:
Data type: carto_volume of S16 - formats : GIS
Data type: genericobject - formats : PYTHON
- AIMS IO types and formats (old API):
Data type: Bucket/DOUBLE - formats : BCK
Data type: Bucket/DTITENSOR - formats : BCK
Data type: Bucket/FIXEDDTMODEL - formats : BCK
Data type: Bucket/FLOAT - formats : BCK
Data type: Bucket/QBALLMODEL - formats : BCK
Data type: Bucket/S16 - formats : BCK
Data type: Bucket/VOID - formats : BCK
Data type: CartoVolume/CDOUBLE - formats : GIS TIFF
Data type: CartoVolume/CFLOAT - formats : GIS TIFF
Data type: CartoVolume/DOUBLE - formats : DICOM FDF GIS MINC NIFTI1 SPM TIFF
Data type: CartoVolume/FLOAT - formats : DICOM ECAT FDF GIS MINC NIFTI1 SPM TIFF VIDA
Data type: CartoVolume/LONG - formats : DICOM GIS MINC SPM
Data type: CartoVolume/POINT3DF - formats : GIS
Data type: CartoVolume/RGB - formats : BMP GIF GIS JPEG JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: CartoVolume/RGBA - formats : BMP GIF GIS JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: CartoVolume/S16 - formats : BMP DICOM ECAT FDF GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: CartoVolume/S32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/S8 - formats : BMP DICOM GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: CartoVolume/U16 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U8 - formats : BMP DICOM FDF GIF GIS JPEG JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/ULONG - formats : DICOM GIS MINC SPM
Data type: CartoVolume/VECTOR_OF_3_S16 - formats : GIS
Data type: CartoVolume/VECTOR_OF_6_FLOAT - formats : GIS
Data type: Graph/VOID - formats : ARG BUNDLES GraphVolume
Data type: Hierarchy/VOID - formats : HIE
Data type: Mesh/VOID - formats : GIFTI MESH PLY POV TRI VRML1
Data type: Mesh4/VOID - formats : MESH PLY POV
Data type: Motion/VOID - formats : TRM
Data type: Segments/VOID - formats : MESH PLY POV
Data type: Texture/FLOAT - formats : GIFTI TEX
Data type: Texture/POINT2DF - formats : GIFTI TEX
Data type: Texture/S16 - formats : GIFTI TEX
Data type: Texture/S32 - formats : GIFTI TEX
Data type: Texture/U32 - formats : GIFTI TEX
Data type: Texture/VECTOR_OF_2_S16 - formats : GIFTI TEX
Data type: Volume/CDOUBLE - formats : GIS TIFF
Data type: Volume/CFLOAT - formats : GIS TIFF
Data type: Volume/DOUBLE - formats : DICOM FDF GIS MINC NIFTI1 SPM TIFF
Data type: Volume/FLOAT - formats : DICOM ECAT FDF GIS MINC NIFTI1 SPM TIFF VIDA
Data type: Volume/LONG - formats : DICOM GIS MINC SPM
Data type: Volume/POINT3DF - formats : GIS
Data type: Volume/RGB - formats : BMP GIF GIS JPEG JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: Volume/RGBA - formats : BMP GIF GIS JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: Volume/S16 - formats : BMP DICOM ECAT FDF GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: Volume/S32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/S8 - formats : BMP DICOM GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: Volume/U16 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U8 - formats : BMP DICOM FDF GIF GIS JPEG JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/ULONG - formats : DICOM GIS MINC SPM
Data type: Volume/VECTOR_OF_3_S16 - formats : GIS
Data type: Volume/VECTOR_OF_6_FLOAT - formats : GIS
Data type: VolumeRef/CDOUBLE - formats : ALLVOLUMES
Data type: VolumeRef/CFLOAT - formats : ALLVOLUMES
Data type: VolumeRef/DOUBLE - formats : ALLVOLUMES
Data type: VolumeRef/FLOAT - formats : ALLVOLUMES
Data type: VolumeRef/LONG - formats : ALLVOLUMES
Data type: VolumeRef/POINT3DF - formats : ALLVOLUMES
Data type: VolumeRef/RGB - formats : ALLVOLUMES
Data type: VolumeRef/RGBA - formats : ALLVOLUMES
Data type: VolumeRef/S16 - formats : ALLVOLUMES
Data type: VolumeRef/S32 - formats : ALLVOLUMES
Data type: VolumeRef/S8 - formats : ALLVOLUMES
Data type: VolumeRef/U16 - formats : ALLVOLUMES
Data type: VolumeRef/U32 - formats : ALLVOLUMES
Data type: VolumeRef/U8 - formats : ALLVOLUMES
Data type: VolumeRef/ULONG - formats : ALLVOLUMES
Data type: VolumeRef/VECTOR_OF_3_S16 - formats : ALLVOLUMES
Data type: VolumeRef/VECTOR_OF_6_FLOAT - formats : ALLVOLUMES
Data type: genericobject/any - formats : PYTHON XML
Data type: object/object - formats : PYTHON XML
- Graph sub-formats readers:
Generic
roi
- AIMS settings:
{
'__syntax__' : 'aims_settings',
'spm_input_radio_convention' : 1,
'spm_input_spm2_normalization' : 1,
'spm_output_radio_convention' : 1,
'spm_output_spm2_normalization' : 1,
'spm_output_4d_volumes' : 1,
'nifti_output_4d_volumes' : 1,
'default_writers' : {
'Mesh' : 'MESH',
'Volume' : 'NIFTI1'
}
}
I will start a new topic for AimsFileConvert
Best regards
Sebastian
I try the third method. I use, as root, "chcon -t texrel_shlib_t /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/lib/*". The dicom conversion is OK.
Here the output of AimsFileInfo --info -verbose 2
libaimsvida.so.3.2.0: libaimsvida.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsvida.so.3.2 successfully loaded.
libaimsdicom.so.3.2.0: libaimsdicom.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsdicom.so.3.2 successfully loaded.
libaimsecat.so.3.2.0: libaimsecat.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsecat.so.3.2 successfully loaded.
libaimsfdf.so.3.2.0: libaimsfdf.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsfdf.so.3.2 successfully loaded.
libaimsjpeg.so.3.2.0: libaimsjpeg.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsjpeg.so.3.2 successfully loaded.
libaimstiff.so.3.2.0: libaimstiff.so.3.2.0: cannot open shared object file: No such file or directory
library libaimstiff.so.3.2 successfully loaded.
libaimsqtformats.so.3.2.0: libaimsqtformats.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsqtformats.so.3.2 successfully loaded.
libaimsminc.so.3.2.0: libaimsminc.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsminc.so.3.2 successfully loaded.
libaimsply.so.3.2.0: libaimsply.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsply.so.3.2 successfully loaded.
libaimsnifti.so.3.2.0: libaimsnifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsnifti.so.3.2 successfully loaded.
libaimsgifti.so.3.2.0: libaimsgifti.so.3.2.0: cannot open shared object file: No such file or directory
library libaimsgifti.so.3.2 successfully loaded.
libconnectomist_aims_plugin.so.3.2.0: libconnectomist_aims_plugin.so.3.2.0: cannot open shared object file: No such file or directory
library libconnectomist_aims_plugin.so.3.2 successfully loaded.
CartoBase version : 3.2.0
AIMS version : 3.2.0
General information:
global shared path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share
aims shared path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share/aims-3.2
mmap path : /tmp
nomenclature path : /usr/local/cartopack-Fedora-4-i686-3.2.0-2009_11_05/share/shfj-3.2/nomenclature
- Compiled with the following built-in options:
VIDA IO : no
JPEG IO : no
DICOM input : no
ECAT IO : no
Plugin support : yes
Plugins:
0 VIDA IO
1 ECAT IO
2 DICOM IO
3 FDF reading
4 JPEG IO
5 TIFF IO
6 Qt image formats IO
7 MINC IO
8 PLY IO
9 NIFTI1 IO
10 GIFTI IO
11 CONNECTOMIST IO
- IO types and formats:
Input formats:
Data type: carto_volume of S16 - formats : GIS
Data type: genericobject - formats : PYTHON XML
Output formats:
Data type: carto_volume of S16 - formats : GIS
Data type: genericobject - formats : PYTHON
- AIMS IO types and formats (old API):
Data type: Bucket/DOUBLE - formats : BCK
Data type: Bucket/DTITENSOR - formats : BCK
Data type: Bucket/FIXEDDTMODEL - formats : BCK
Data type: Bucket/FLOAT - formats : BCK
Data type: Bucket/QBALLMODEL - formats : BCK
Data type: Bucket/S16 - formats : BCK
Data type: Bucket/VOID - formats : BCK
Data type: CartoVolume/CDOUBLE - formats : GIS TIFF
Data type: CartoVolume/CFLOAT - formats : GIS TIFF
Data type: CartoVolume/DOUBLE - formats : DICOM FDF GIS MINC NIFTI1 SPM TIFF
Data type: CartoVolume/FLOAT - formats : DICOM ECAT FDF GIS MINC NIFTI1 SPM TIFF VIDA
Data type: CartoVolume/LONG - formats : DICOM GIS MINC SPM
Data type: CartoVolume/POINT3DF - formats : GIS
Data type: CartoVolume/RGB - formats : BMP GIF GIS JPEG JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: CartoVolume/RGBA - formats : BMP GIF GIS JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: CartoVolume/S16 - formats : BMP DICOM ECAT FDF GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: CartoVolume/S32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/S8 - formats : BMP DICOM GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: CartoVolume/U16 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/U8 - formats : BMP DICOM FDF GIF GIS JPEG JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: CartoVolume/ULONG - formats : DICOM GIS MINC SPM
Data type: CartoVolume/VECTOR_OF_3_S16 - formats : GIS
Data type: CartoVolume/VECTOR_OF_6_FLOAT - formats : GIS
Data type: Graph/VOID - formats : ARG BUNDLES GraphVolume
Data type: Hierarchy/VOID - formats : HIE
Data type: Mesh/VOID - formats : GIFTI MESH PLY POV TRI VRML1
Data type: Mesh4/VOID - formats : MESH PLY POV
Data type: Motion/VOID - formats : TRM
Data type: Segments/VOID - formats : MESH PLY POV
Data type: Texture/FLOAT - formats : GIFTI TEX
Data type: Texture/POINT2DF - formats : GIFTI TEX
Data type: Texture/S16 - formats : GIFTI TEX
Data type: Texture/S32 - formats : GIFTI TEX
Data type: Texture/U32 - formats : GIFTI TEX
Data type: Texture/VECTOR_OF_2_S16 - formats : GIFTI TEX
Data type: Volume/CDOUBLE - formats : GIS TIFF
Data type: Volume/CFLOAT - formats : GIS TIFF
Data type: Volume/DOUBLE - formats : DICOM FDF GIS MINC NIFTI1 SPM TIFF
Data type: Volume/FLOAT - formats : DICOM ECAT FDF GIS MINC NIFTI1 SPM TIFF VIDA
Data type: Volume/LONG - formats : DICOM GIS MINC SPM
Data type: Volume/POINT3DF - formats : GIS
Data type: Volume/RGB - formats : BMP GIF GIS JPEG JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: Volume/RGBA - formats : BMP GIF GIS JPEG(Qt) MNG PBM PGM PNG PPM TIFF XBM XPM
Data type: Volume/S16 - formats : BMP DICOM ECAT FDF GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF VIDA XBM XPM
Data type: Volume/S32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/S8 - formats : BMP DICOM GENESIS GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM XBM XPM
Data type: Volume/U16 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U32 - formats : BMP DICOM FDF GIF GIS JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/U8 - formats : BMP DICOM FDF GIF GIS JPEG JPEG(Qt) MINC MNG NIFTI1 PBM PGM PNG PPM SPM TIFF XBM XPM
Data type: Volume/ULONG - formats : DICOM GIS MINC SPM
Data type: Volume/VECTOR_OF_3_S16 - formats : GIS
Data type: Volume/VECTOR_OF_6_FLOAT - formats : GIS
Data type: VolumeRef/CDOUBLE - formats : ALLVOLUMES
Data type: VolumeRef/CFLOAT - formats : ALLVOLUMES
Data type: VolumeRef/DOUBLE - formats : ALLVOLUMES
Data type: VolumeRef/FLOAT - formats : ALLVOLUMES
Data type: VolumeRef/LONG - formats : ALLVOLUMES
Data type: VolumeRef/POINT3DF - formats : ALLVOLUMES
Data type: VolumeRef/RGB - formats : ALLVOLUMES
Data type: VolumeRef/RGBA - formats : ALLVOLUMES
Data type: VolumeRef/S16 - formats : ALLVOLUMES
Data type: VolumeRef/S32 - formats : ALLVOLUMES
Data type: VolumeRef/S8 - formats : ALLVOLUMES
Data type: VolumeRef/U16 - formats : ALLVOLUMES
Data type: VolumeRef/U32 - formats : ALLVOLUMES
Data type: VolumeRef/U8 - formats : ALLVOLUMES
Data type: VolumeRef/ULONG - formats : ALLVOLUMES
Data type: VolumeRef/VECTOR_OF_3_S16 - formats : ALLVOLUMES
Data type: VolumeRef/VECTOR_OF_6_FLOAT - formats : ALLVOLUMES
Data type: genericobject/any - formats : PYTHON XML
Data type: object/object - formats : PYTHON XML
- Graph sub-formats readers:
Generic
roi
- AIMS settings:
{
'__syntax__' : 'aims_settings',
'spm_input_radio_convention' : 1,
'spm_input_spm2_normalization' : 1,
'spm_output_radio_convention' : 1,
'spm_output_spm2_normalization' : 1,
'spm_output_4d_volumes' : 1,
'nifti_output_4d_volumes' : 1,
'default_writers' : {
'Mesh' : 'MESH',
'Volume' : 'NIFTI1'
}
}
I will start a new topic for AimsFileConvert
Best regards
Sebastian