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help > RE: smoothed fmri data in roi-roi analyses
Feb 18, 2015 04:02 PM | Alfonso Nieto-Castanon - Boston University
RE: smoothed fmri data in roi-roi analyses
Hi Peter,
There are a few things missing/strange in your script (e.g. the variable 'n' I imagine is perhaps in a loop across all of your subjects, the variable 'dir' probably points to the subject-specific directory, the fields 'Setup.nsubjects' should indicate the total number of subjects, the field 'Setup.roiextract' only needs to be defined once, not for each subject, etc.). Other than these, if you are selecting the 'u*.img' files as source of functional volumes for your ROI-to-ROI native-space analyses, then the roiextract rule can be simply set to 1 (to use those same volumes for ROI extraction) instead of using the specified rule in your script ('^sw','') which is expecting functional volumes to be normalized and smoothed and specifying that it should use instead the un-normalized un-smoothed volumes for ROI extraction).
Hope this helps clarify
Alfonso
Originally posted by Peter McColgan:
There are a few things missing/strange in your script (e.g. the variable 'n' I imagine is perhaps in a loop across all of your subjects, the variable 'dir' probably points to the subject-specific directory, the fields 'Setup.nsubjects' should indicate the total number of subjects, the field 'Setup.roiextract' only needs to be defined once, not for each subject, etc.). Other than these, if you are selecting the 'u*.img' files as source of functional volumes for your ROI-to-ROI native-space analyses, then the roiextract rule can be simply set to 1 (to use those same volumes for ROI extraction) instead of using the specified rule in your script ('^sw','') which is expecting functional volumes to be normalized and smoothed and specifying that it should use instead the un-normalized un-smoothed volumes for ROI extraction).
Hope this helps clarify
Alfonso
Originally posted by Peter McColgan:
Thanks Alfonso, so when I am batch scripting for
an ROI-ROI analysis in native space is the following correct;
BATCH.Setup.nsubjects=n;
for i= 1:161
f=spm_select('FPList',dir, '^u.*\.img$');
BATCH.Setup.functionals{n}{1}{i}=f(i,:);
end
BATCH.Setup.structurals{n}=fullfile(root,sub_ind{n},'T1_Data','seg4coreg.nii');
%BATCH.Setup.roiextract=1;
BATCH.Setup.roiextract=3;
batch.Setup.roiextract_rule = {1, '^sw', ''};
Best wishes,
Peter
BATCH.Setup.nsubjects=n;
for i= 1:161
f=spm_select('FPList',dir, '^u.*\.img$');
BATCH.Setup.functionals{n}{1}{i}=f(i,:);
end
BATCH.Setup.structurals{n}=fullfile(root,sub_ind{n},'T1_Data','seg4coreg.nii');
%BATCH.Setup.roiextract=1;
BATCH.Setup.roiextract=3;
batch.Setup.roiextract_rule = {1, '^sw', ''};
Best wishes,
Peter
Threaded View
| Title | Author | Date |
|---|---|---|
| Peter McColgan | Jan 30, 2015 | |
| Alfonso Nieto-Castanon | Feb 8, 2015 | |
| Kaylah Curtis | Nov 11, 2016 | |
| Alfonso Nieto-Castanon | Nov 12, 2016 | |
| Larry Lai | Apr 1, 2018 | |
| Peter McColgan | Feb 13, 2015 | |
| Alfonso Nieto-Castanon | Feb 18, 2015 | |