Anatomic pipeline problems

pvdemael · Post by **pvdemael** » Tue Sep 14, 2004 1:45 pm

Hello,

I imported an anatomic image which has been normalised using spm
When running the Anatomic pipeline, I get the following messages. What is going wrong or what am I doing wrong?
Is it the image size (79x100x68)?

Pieter

Process Ana Do A Lot of Things from T1 MRI 2 started
Ana Brain Mask from T1 MRI 2
Vip Bias Correction 2
VipBiasCorrection
Vip Histogram analysis 2
VipHistoAnalysis
Vip Get Brain 2
VipGetBrain

------------------------------
! VIP Warning:
Something was wrong with the iterative erosion!
------------------------------
Ana Split Brain from Brain Mask 2
Vip Split Brain 2
VipSplitBrain
Ana Compute Hemi Grey White Classification 2
Computing left hemisphere grey-white classification...
VipGreyWhiteClassif
Can not open this image: c:\Data\database\Patienten\Patient18\segment\voronoi_Patient18
Computing right hemisphere grey-white classification...
VipGreyWhiteClassif
Can not open this image: c:\Data\database\Patienten\Patient18\segment\voronoi_Patient18
Ana Get Opened Hemi Surface 2
Masking Bias corrected image with left hemisphere mask...
VipMask
Can not open this image: c:\Data\database\Patienten\Patient18\segment\voronoi_Patient18
Detecting left grey/white interface...
VipHomotopicSnake
Can not open this image: C:\WINDOWS\TEMP\neuro2004_212
Reconstructing left hemisphere surface...
VipSingleThreshold
Can not open this image: c:\Data\database\Patienten\Patient18\segment\Lcortex_Patient18
VipOpenFold
Can not open this image: C:\WINDOWS\TEMP\neuro2004_212
Triangulation and Decimation...
AimsMeshBrain

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Masking Bias corrected image with right hemisphere mask...
VipMask
Can not open this image: c:\Data\database\Patienten\Patient18\segment\voronoi_Patient18
Detecting right grey/white interface...
VipHomotopicSnake
Can not open this image: C:\WINDOWS\TEMP\neuro2004_225
Reconstructing right hemisphere surface...
VipSingleThreshold
Can not open this image: c:\Data\database\Patienten\Patient18\segment\Rcortex_Patient18
VipOpenFold
Can not open this image: C:\WINDOWS\TEMP\neuro2004_225
Triangulation and Decimation...
AimsMeshBrain

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Ana Get Spherical Cortical Surface 2
New cubic spatial resolution:2
Computing oversampled MR image to improve cortical surface definition (cubic spline)
VipSplineResamp
Computing oversampled voronoi diagram (nearest neighbor)
VipSplineResamp
Can not open this image: c:\Data\database\Patienten\Patient18\segment\voronoi_Patient18
Masking Bias corrected image with left hemisphere mask...
VipMask
Can not open this image: C:\WINDOWS\TEMP\neuro2004_242
Detecting left grey/white interface...
VipHomotopicSnake
Can not open this image: C:\WINDOWS\TEMP\neuro2004_247
Reconstructing left hemisphere white surface...
VipSingleThreshold
Can not open this image: C:\WINDOWS\TEMP\neuro2004_250
Triangulation and Decimation...
AimsMeshWhite

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Smoothing mesh...
Mesh smoothing 3
AimsMeshSmoothing

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Masking Bias corrected image with right hemisphere mask...
VipMask
Can not open this image: C:\WINDOWS\TEMP\neuro2004_242
Detecting right grey/white interface...
VipHomotopicSnake
Can not open this image: C:\WINDOWS\TEMP\neuro2004_263
Reconstructing right hemisphere white surface...
VipSingleThreshold
Can not open this image: C:\WINDOWS\TEMP\neuro2004_266
Triangulation and Decimation...
AimsMeshWhite

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Smoothing mesh...
Mesh smoothing 4
AimsMeshSmoothing

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Head Mesh 2
VipGetHead
AimsMeshBrain
Ana Compute Cortical Fold Arg 2
Masking Bias corrected image with hemisphere masks...
VipMask
Can not open this image: c:\Data\database\Patienten\Patient18\segment\voronoi_Patient18
VipMask
Can not open this image: c:\Data\database\Patienten\Patient18\segment\voronoi_Patient18
Detecting left grey/white interface...
VipHomotopicSnake
Can not open this image: C:\WINDOWS\TEMP\neuro2004_290
Computing skeleton and buried gyrus watershed...
VipSkeleton
Can not open this image: c:\Data\database\Patienten\Patient18\segment\Lcortex_Patient18
Building Attributed Relational Graph...
VipFoldArg
Can not open this image: c:\Data\database\Patienten\Patient18\segment\Lskeleton_Patient18
VipFoldArgAtt
Can not open this image: c:\Data\database\Patienten\Patient18\segment\Lskeleton_Patient18
VipFoldArg
Can not open file c:\Data\database\Patienten\Patient18\graphe\LPatient18.ss.Vip

------------------------------
!! VIP Error:

Execution aborted in function 'VipOldReadSSfile'.

------------------------------
AimsGraphConvert
c:\Data\database\Patienten\Patient18\graphe\LPatient18local.arg : format error
computing additional attributes
AimsGraphComplete
c:\Data\database\Patienten\Patient18\graphe\LPatient18.arg : format error
Detecting right grey/white interface...
VipHomotopicSnake
Can not open this image: C:\WINDOWS\TEMP\neuro2004_293
Computing skeleton and buried gyrus watershed...
VipSkeleton
Can not open this image: c:\Data\database\Patienten\Patient18\segment\Rcortex_Patient18
Building Attributed Relational Graph...
VipFoldArg
Can not open this image: c:\Data\database\Patienten\Patient18\segment\Rskeleton_Patient18
VipFoldArgAtt
Can not open this image: c:\Data\database\Patienten\Patient18\segment\Rskeleton_Patient18
VipFoldArg
Can not open file c:\Data\database\Patienten\Patient18\graphe\RPatient18.ss.Vip

------------------------------
!! VIP Error:

Execution aborted in function 'VipOldReadSSfile'.

------------------------------
AimsGraphConvert
c:\Data\database\Patienten\Patient18\graphe\RPatient18local.arg : format error
computing additional attributes
AimsGraphComplete
c:\Data\database\Patienten\Patient18\graphe\RPatient18.arg : format error
Graph To Talairach converter 2
AimsGraphExtractTransformation
unrecognized format
Process Ana Do A Lot of Things from T1 MRI 2 finished

Jean-Francois Mangin · Tue Sep 14, 2004 5:08 pm

Did you manage to use the lesson1 data provided on our web site to check your install is OK?
Did you process some other dataset the same way?
Did you normalize your data to a 1mm spatial resolution? I am afraid not when I see the size of your file. High resolution is required to deal with the cortex resolution...
Did you provide the AC PC location manually or with the menu (this menu, I am afraid, is dedicated to the parameters used in the SHFJ)?

Post by **riviere** » Fri Sep 17, 2004 8:04 am

79x100x68 is rather small. Typical images are 256x256x124, and normalized SPM images are about 160x190x130. Your image seems to be twice as small, or have a resolution twice bigger. What is the voxel size ? Segmentation is possible with voxels of about 1mm. If your image has 2mm resolution, it is probably not possible to obtain something correct from it.

Denis

PeterK · Post by **PeterK** » Thu Sep 30, 2004 7:18 pm

riviere wrote:79x100x68 is rather small. Typical images are 256x256x124, and normalized SPM images are about 160x190x130. Your image seems to be twice as small, or have a resolution twice bigger. What is the voxel size ? Segmentation is possible with voxels of about 1mm. If your image has 2mm resolution, it is probably not possible to obtain something correct from it.

Denis

I bet that is the case. Especially if the image wasn't skullped - the 2x2x2 reslicing basically removed the band of CSF that is used for skull stripping.