Hi Doug,
I am able to run mri_segstats with slabel below, but it is finding two
segmentations in my label and producing a column for each. one is associated
with an ID of 0 and one is associated with an ID of 1. I assume that I want the
2nd column (the ID of 1). What is the command doing? Is it creating one
segmentation out of my label and one out of the rest of the cortical surface?
Also, could you please address the 3rd question from the email below? Thanks so
much!
Best,
Emily
On Mar 28, 2014, at 12:37 PM, Douglas N Greve wrote:
>
> On 03/28/2014 12:04 PM, Emily Boeke wrote:
>> 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
> What I mean is that the ROI used is that of the native subject, not
> fsaverage. If you were to map the hippocampus to fsaverage and overlay it
> with the hippo of fsaverage you would see that they are different. FSFAST
> resamples the time series data into fsaverage/mni space and computes all the
> stats there, so the ROI boundaries need to be transferred to that 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.)
>
> You can't swap them out. Read the docs for it.
>> 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/
>>>
>>>
>>
>>
>
> --
> 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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