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help > RE: subject specific ROIs
Dec 5, 2014 01:12 AM | Alfonso Nieto-Castanon - Boston University
RE: subject specific ROIs
Hi Eric,
Yes, that should work perfectly fine, only a couple of comments:
1) the indexes in your example might be incorrect, the indexes should be batch.Setup.rois.files{ROI_NUMBER}{SUBJECT_NUMBER} instead of batch.Setup.rois.files{SUBJECT_NUMBER}{ROI_NUMBER} as your example would seem to suggest
2) since your ROIs are defined in subject-space you need to make sure that the BOLD signals are extracted from the appropriate (subject-space) functional volumes, instead of the (typically) MNI-space functional volumes necessary for voxel-based analyses. To that end you could use for example something like:
batch.Setup.roiextract = 3; % manually-defined rule
batch.Setup.roiextract_rule = {1, '^sw', ''};
(if your functional volumes defined in batch.Setup.functionals are in MNI space and are named 'swauFunctionals.nii', for example, this rule will consider instead the files named 'auFunctionals.nii' -in subject-space- when CONN needs to extract BOLD-signals from your ROIs; see help conn_batch for more details)
Last, regarding keeping the original MNI-space seeds, in general you can simply add those to your list of ROIs, for example:
batch.Setup.rois.names={'L_Amygdala', 'R_Amygdala', 'dmn'};
...
batch.Setup.rois.files{3}='/software/conn/rois/dmn.nii';
but considering the point (2) above, I would probably also add the line:
batch.Setup.rois.roiextract = [1 1 0];
to make sure that the BOLD-signal for these particular ROIs is extracted from appropriately MNI-space volumes instead (I am assuming here that in batch.Setup.functionals you are entering the MNI-space volumes, e.g. swauFunctionals.nii files).
Hope this helps and let me know if you would like me to further clarify any of this
Alfonso
Originally posted by eric Porges:
Yes, that should work perfectly fine, only a couple of comments:
1) the indexes in your example might be incorrect, the indexes should be batch.Setup.rois.files{ROI_NUMBER}{SUBJECT_NUMBER} instead of batch.Setup.rois.files{SUBJECT_NUMBER}{ROI_NUMBER} as your example would seem to suggest
2) since your ROIs are defined in subject-space you need to make sure that the BOLD signals are extracted from the appropriate (subject-space) functional volumes, instead of the (typically) MNI-space functional volumes necessary for voxel-based analyses. To that end you could use for example something like:
batch.Setup.roiextract = 3; % manually-defined rule
batch.Setup.roiextract_rule = {1, '^sw', ''};
(if your functional volumes defined in batch.Setup.functionals are in MNI space and are named 'swauFunctionals.nii', for example, this rule will consider instead the files named 'auFunctionals.nii' -in subject-space- when CONN needs to extract BOLD-signals from your ROIs; see help conn_batch for more details)
Last, regarding keeping the original MNI-space seeds, in general you can simply add those to your list of ROIs, for example:
batch.Setup.rois.names={'L_Amygdala', 'R_Amygdala', 'dmn'};
...
batch.Setup.rois.files{3}='/software/conn/rois/dmn.nii';
but considering the point (2) above, I would probably also add the line:
batch.Setup.rois.roiextract = [1 1 0];
to make sure that the BOLD-signal for these particular ROIs is extracted from appropriately MNI-space volumes instead (I am assuming here that in batch.Setup.functionals you are entering the MNI-space volumes, e.g. swauFunctionals.nii files).
Hope this helps and let me know if you would like me to further clarify any of this
Alfonso
Originally posted by eric Porges:
We are attempting to load subject specific ROIs
(from Freesurfer), in the subject's native t1 space via the batch
interface (this is from 2 subjects, more will be added).
batch.Setup.rois.names={'L_Amygdala', 'R_Amygdala'}; % put ROI names here
batch.Setup.rois.files{1}{1}=fullfile('/lfs/scratch/rlts/cam/working/cam_scratch/ot_rsbold_batch_test/11001/','11001_l_amygdala.nii');
batch.Setup.rois.files{1}{2}=fullfile('/lfs/scratch/rlts/cam/working/cam_scratch/ot_rsbold_batch_test/11001/','11001_r_amygdala.nii');
batch.Setup.rois.files{2}{1}=fullfile('/lfs/scratch/rlts/cam/working/cam_scratch/ot_rsbold_batch_test/11002/','11002_l_amygdala.nii');
batch.Setup.rois.files{2}{2}=fullfile('/lfs/scratch/rlts/cam/working/cam_scratch/ot_rsbold_batch_test/11002/','11002_r_amygdala.nii');
We intend to use this for group, seed to seed & seed to voxel analysis. Should this work?
Is there a way to add these and keep the defualt rsREL, LLP, MPFC. PCC, etc seeds? As we have currently implemented it, we get these ROIs but no longer have the default one.
Thanks!
batch.Setup.rois.names={'L_Amygdala', 'R_Amygdala'}; % put ROI names here
batch.Setup.rois.files{1}{1}=fullfile('/lfs/scratch/rlts/cam/working/cam_scratch/ot_rsbold_batch_test/11001/','11001_l_amygdala.nii');
batch.Setup.rois.files{1}{2}=fullfile('/lfs/scratch/rlts/cam/working/cam_scratch/ot_rsbold_batch_test/11001/','11001_r_amygdala.nii');
batch.Setup.rois.files{2}{1}=fullfile('/lfs/scratch/rlts/cam/working/cam_scratch/ot_rsbold_batch_test/11002/','11002_l_amygdala.nii');
batch.Setup.rois.files{2}{2}=fullfile('/lfs/scratch/rlts/cam/working/cam_scratch/ot_rsbold_batch_test/11002/','11002_r_amygdala.nii');
We intend to use this for group, seed to seed & seed to voxel analysis. Should this work?
Is there a way to add these and keep the defualt rsREL, LLP, MPFC. PCC, etc seeds? As we have currently implemented it, we get these ROIs but no longer have the default one.
Thanks!
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| Title | Author | Date |
|---|---|---|
| eric Porges | Dec 4, 2014 | |
| Alfonso Nieto-Castanon | Dec 5, 2014 | |