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/
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
