Hi Doug,
Thanks for the response.
Regarding #1, I am still confused. if the ROI boundaries computed in native
space are mapped to fsaverage/mni305 space, doesn't that mean the actual
computing of the averages is done in fsaverage/mni305 space? Why would mapping
to fsaverage/mni305 space be necessary in the ROI analysis if the averages are
computed in native space?
Regarding #2, I tried that already and got the error "must specify an output
table file" (I used the exact same command, just swapping out -slabel for
-seg.) Also, this analysis is purely done in mni305/fsaverage space because it
is using the concatenated file, correct? If I want to do it in native space,
would I use label to label (as written below) and then funcroi? Do you think it
would make a difference either way?
mri_label2label --srclabel ${SUBJECTS_DIR}/fsaverage/label/mylabel.label --src
subject fsaverage --trglabel ${SUBJECTS_DIR}/subject/label/mylabel.label
--trgsubject subject -regmethod surface --hemi lh
Thanks,
Emily
On Mar 28, 2014, at 11:15 AM, Douglas N Greve wrote:
>
> On 03/28/2014 08:51 AM, Emily Boeke wrote:
>> Hi Freesurfers,
>>
>> I have some questions about ROI analyses.
>>
>> 1. I use the mni305 and fsaverage flags during preprocessing. Does this mean
>> that when I run funcroi-config, funcroi-sess, etc, the analysis is being
>> done for each subject in mni305 space, as opposed to native space? Meaning,
>> If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will not be
>> done using the left amygdala from that individual's aseg, but instead will
>> be done in mni305 space with the fsaverage left amygdala ROI?
> No, it is done in native space. The voxelwise analysis is done in
> fsaverage/mni305 space, but the ROI boundaries used to compute the ROI
> averages are computed in native space and mapped to fsaverage/mni305 space.
>>
>> 2. I sometimes want to use labels I've created on fsaverage from averaged
>> group activation to do ROI analyses. If the ROI is in the volume, I convert
>> the label to a mask and run:
>>
>> mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf ces.mymask.dat
>>
>> In the appropriate contrast folder. What should I do if I want to do the
>> same thing, but with a surface label (in a lh or rh surface analysis, not an
>> mni305 analysis)?
> You can still use mri_segstats, just spec --slabel instead of seg
> doug
>>
>> Thanks!
>>
>> Emily
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [email protected]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
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