help > Atlased file availability
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Mar 20, 2012 06:03 PM | Farras Abdelnour
Atlased file availability
Dear all,
Regarding my last posting titled "Starting with realigned/registered images," it appears that the issue was one of missing masks, which I accounted for using the following lines:
process_fmri
% Setup grey/white/CSF masks:
BATCH.Setup.masks.Grey.files{1} = GreyMask;
BATCH.Setup.masks.White.files{1} = WhiteMask;
BATCH.Setup.masks.CSF.files{1} = CSFMask;
My question now is, if I already have the subject's Atlased image, is there a way to use the altased file directly and skip the steps of the mask files?
With thanks,
farras
Regarding my last posting titled "Starting with realigned/registered images," it appears that the issue was one of missing masks, which I accounted for using the following lines:
process_fmri
% Setup grey/white/CSF masks:
BATCH.Setup.masks.Grey.files{1} = GreyMask;
BATCH.Setup.masks.White.files{1} = WhiteMask;
BATCH.Setup.masks.CSF.files{1} = CSFMask;
My question now is, if I already have the subject's Atlased image, is there a way to use the altased file directly and skip the steps of the mask files?
With thanks,
farras
Mar 20, 2012 10:03 PM | Alfonso Nieto-Castanon - Boston University
RE: Atlased file availability
Dear Farras,
Unfortunatelly the toolbox expects to have these as separate mask files (but this is a perfectly reasonable request so I will try to incorporate this option in the next release of the toolbox). In the meantime perhaps you could use the following command to create the individual grey/white/csf masks from your atlas file (and then enter the resulting files into the Grey/White/CSF fields of BATCH.Setup.masks).
filename='/data/atlasfile.img';
roinumbers=[1,2,3];
rex(filename,filename,'gui',false,'level','clusters','output_type','save','output_files','roi#.img','select_clusters',false,'selected_clusters',roinumbers);
changing the first line to point to the name of your atlas .img file, and changing the second line to indicate the numbers associated with your grey/white/csf areas in your atlas file. This will generate three files (named [filename].rex.roi1 to [filename].rex.roi3) containing the individual mask files that you may then enter into the BATCH.Setup.masks fields (you should repeat this for each subject).
Hope this helps
Alfonso
Originally posted by Farras Abdelnour:
Unfortunatelly the toolbox expects to have these as separate mask files (but this is a perfectly reasonable request so I will try to incorporate this option in the next release of the toolbox). In the meantime perhaps you could use the following command to create the individual grey/white/csf masks from your atlas file (and then enter the resulting files into the Grey/White/CSF fields of BATCH.Setup.masks).
filename='/data/atlasfile.img';
roinumbers=[1,2,3];
rex(filename,filename,'gui',false,'level','clusters','output_type','save','output_files','roi#.img','select_clusters',false,'selected_clusters',roinumbers);
changing the first line to point to the name of your atlas .img file, and changing the second line to indicate the numbers associated with your grey/white/csf areas in your atlas file. This will generate three files (named [filename].rex.roi1 to [filename].rex.roi3) containing the individual mask files that you may then enter into the BATCH.Setup.masks fields (you should repeat this for each subject).
Hope this helps
Alfonso
Originally posted by Farras Abdelnour:
Dear all,
Regarding my last posting titled "Starting with realigned/registered images," it appears that the issue was one of missing masks, which I accounted for using the following lines:
process_fmri
% Setup grey/white/CSF masks:
BATCH.Setup.masks.Grey.files{1} = GreyMask;
BATCH.Setup.masks.White.files{1} = WhiteMask;
BATCH.Setup.masks.CSF.files{1} = CSFMask;
My question now is, if I already have the subject's Atlased image, is there a way to use the altased file directly and skip the steps of the mask files?
With thanks,
farras
Regarding my last posting titled "Starting with realigned/registered images," it appears that the issue was one of missing masks, which I accounted for using the following lines:
process_fmri
% Setup grey/white/CSF masks:
BATCH.Setup.masks.Grey.files{1} = GreyMask;
BATCH.Setup.masks.White.files{1} = WhiteMask;
BATCH.Setup.masks.CSF.files{1} = CSFMask;
My question now is, if I already have the subject's Atlased image, is there a way to use the altased file directly and skip the steps of the mask files?
With thanks,
farras
Mar 20, 2012 11:03 PM | Farras Abdelnour
RE: Atlased file availability
Dear Alfonso,
Thank you very much for your help. I will go ahead and implement your suggestion.
Best,
farras
Thank you very much for your help. I will go ahead and implement your suggestion.
Best,
farras