Use --id 1 or --excludeid 0 with mri_segstats. 3rd question answered below.
On 04/01/2014 10:42 AM, Emily Boeke wrote:
> 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?
I think you can do it in native space if you specify native when you run
mkanalysis-sess
doug
>>>
>>> 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/
>>
>>
>
>
--
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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