Hello everyone.
I need your help.
Can I load the MNC files with BrainVisa?
If is there any procedure in BrainVisa package to import this kind of image please can you help me how to use it?
Sincerely and best regards.
Yasser
Load MNC files with BrainVisa(?)
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Yasser_Aleman
- Posts: 10
- Joined: Fri Oct 15, 2004 5:07 pm
- Location: Cuban Neuroscience Center
Hi,
In theory, module of anatomy importation can take into account this format and to convert it in GIS format. But I never try with this format.
This treatment is locate here : 'data managment -> import -> anatomy -> import T1 MRI'.
If you use this treatment you must at least have one data-base in BrainVISA. You can do this with : 'Preferences --> Database'. You click on 'Add' and you indicate a directory for the database (Hierarchy and Cache are not mandatory).
Next, you can import data in BrainVISA with the treatment. When you will select it in right window you can read documentation.
Try and say me if you could do it!
Isabelle
In theory, module of anatomy importation can take into account this format and to convert it in GIS format. But I never try with this format.
This treatment is locate here : 'data managment -> import -> anatomy -> import T1 MRI'.
If you use this treatment you must at least have one data-base in BrainVISA. You can do this with : 'Preferences --> Database'. You click on 'Add' and you indicate a directory for the database (Hierarchy and Cache are not mandatory).
Next, you can import data in BrainVISA with the treatment. When you will select it in right window you can read documentation.
Try and say me if you could do it!
Isabelle
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Yasser_Aleman
- Posts: 10
- Joined: Fri Oct 15, 2004 5:07 pm
- Location: Cuban Neuroscience Center
Here again
Hi again Isabelle.
I did everything that you told me to do but the import package show me this error.
Exception: E:\icbm_brains\mni_icbm_00100_6396000_t1.mnc is not a valid file for type Raw T1 MRI and format list ['GIS image', 'SPM image', 'VIDA image', 'ECAT v image', 'ECAT i image', 'JPEG image', 'DICOM image']
Maybe I am doing something wrong but for me it means that Brainvisa software can't load this kind of images. Do you think the same?
I think that in SPM toolbox we can import Montreal Neurological Institute images(the extension is .mnc) to analyze format. After this we can introduce them to BrainVisa and process them.
I am not sure about this and if this import process can introduce some errors to the images.
Tell me your opinion about this and if I am making some mistakes or any step that I have to do before introducing teh images please tell me.
I hope you request.
Sincerely and best regards to you.
Yasser
I did everything that you told me to do but the import package show me this error.
Exception: E:\icbm_brains\mni_icbm_00100_6396000_t1.mnc is not a valid file for type Raw T1 MRI and format list ['GIS image', 'SPM image', 'VIDA image', 'ECAT v image', 'ECAT i image', 'JPEG image', 'DICOM image']
Maybe I am doing something wrong but for me it means that Brainvisa software can't load this kind of images. Do you think the same?
I think that in SPM toolbox we can import Montreal Neurological Institute images(the extension is .mnc) to analyze format. After this we can introduce them to BrainVisa and process them.
I am not sure about this and if this import process can introduce some errors to the images.
Tell me your opinion about this and if I am making some mistakes or any step that I have to do before introducing teh images please tell me.
I hope you request.
Sincerely and best regards to you.
Yasser
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Yasser_Aleman
- Posts: 10
- Joined: Fri Oct 15, 2004 5:07 pm
- Location: Cuban Neuroscience Center
Hi again Isabelle.
Yes I did it.
I used some SPM scripts implemented in SPM2 toolbox and convert the image from .mnc to img and after that I introduced the image in Brainvisa and It works without any inconvenient.
Thanks for your help and if you want the scrip I can send it to you by e -mail.
Now I have another doubt.
Can I run multiple subjets one by one automatically in Brainvisa?
I mean, If I have lots of subjects and I want to process all that images is there any procedure in Brainvisa to do it?
I hope that you can help me. And sorry about my insistence.
Sincerely and best regards to you.
Yasser
Yes I did it.
I used some SPM scripts implemented in SPM2 toolbox and convert the image from .mnc to img and after that I introduced the image in Brainvisa and It works without any inconvenient.
Thanks for your help and if you want the scrip I can send it to you by e -mail.
Now I have another doubt.
Can I run multiple subjets one by one automatically in Brainvisa?
I mean, If I have lots of subjects and I want to process all that images is there any procedure in Brainvisa to do it?
I hope that you can help me. And sorry about my insistence.
Sincerely and best regards to you.
Yasser
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Jean-Francois Mangin
- Posts: 337
- Joined: Mon Mar 01, 2004 10:24 am
- Location: Neurospin, CEA, France
- Contact:
Hi,
In fact, it is a temporary procedure for mnc format .... Perhaps we will have more informations next week.
Yes, there is a iterate mode. There is 'iterate button' near 'run buton'. The procedure is :
- Open a process BrainVISA (like Ana Do A lot of ...)
- Click on 'iterate button' --> a new window (1) is displayed
- Click on '...' button for T1mri --> a new selecter (1) is displayed
- Click on 'green magnifying glass' --> a new selecter (2) is displayed
- Select several T1mri in your database and click OK
- Click Ok to leave selecter (1)
- Now we are on window (1) , and only the line of T1mri is not empty
- Click on 'OK' of window (1)
- Now we are on initial process, and you can observe a new slider on the right. If you use it, you can move on selected T1mri.
- And now you can click on 'run button' !
Isabelle
In fact, it is a temporary procedure for mnc format .... Perhaps we will have more informations next week.
Yes, there is a iterate mode. There is 'iterate button' near 'run buton'. The procedure is :
- Open a process BrainVISA (like Ana Do A lot of ...)
- Click on 'iterate button' --> a new window (1) is displayed
- Click on '...' button for T1mri --> a new selecter (1) is displayed
- Click on 'green magnifying glass' --> a new selecter (2) is displayed
- Select several T1mri in your database and click OK
- Click Ok to leave selecter (1)
- Now we are on window (1) , and only the line of T1mri is not empty
- Click on 'OK' of window (1)
- Now we are on initial process, and you can observe a new slider on the right. If you use it, you can move on selected T1mri.
- And now you can click on 'run button' !
Isabelle
-
riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Hi,
Minc format support is not in the current stable version. It is a new module (developed by Olivier Coliot in Montreal) which is only in the current development version (and has still some limitations such as no 4D support).
So just wait and use an external software at the moment... SPM2 handles minc format (SPM99 doesn't).
Denis
Minc format support is not in the current stable version. It is a new module (developed by Olivier Coliot in Montreal) which is only in the current development version (and has still some limitations such as no 4D support).
So just wait and use an external software at the moment... SPM2 handles minc format (SPM99 doesn't).
Denis