External Email - Use Caution Hi Doug,
We actually do want the voxel-by-voxel results. Could you please give details on how we would do that? Specifically, would we need to use the command line to run the Welch's T/F or would we extract values for each voxel and put them into another software to conduct the Welch's T/F? Thank you again. Greve, Douglas N.,Ph.D. <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Greve%2C+Douglas+N.%2CPh.D.%22> Thu, 14 Mar 2019 08:45:56 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20190314> You can use mri_segstats to get whole-cortex means (use --slabel and specify the lh.cortex.label and add --id 1). You can do the same thing with the variances. The problem with doing it after mri_glmfit is that the variances will not reflect the spatial averaging over cortex. If you really just want one number for cortex, you should use mri_segstats to extract the mean values from the stack (ie, the --y input), using --avgwf. This will give you a column of numbers, one mean for each subject. Then you can process this however you want. When I first responded, I thought that you want to do this on a voxel-wise basis. doug On Thu, Mar 14, 2019 at 10:10 AM Hannah CK <hckal...@gmail.com> wrote: > Hi Dr. Greve, > > Sorry about that - I had followed the "Reply via email" link on the archive > page instead of posting to the forum directly. > > Thank you for this response. Can extracting the means be done at the > whole-brain level? If we get the means and variances for each group, I'm > assuming we would need to use ROIs. Could you please clarify whether it's > possible to extract means across the whole brain? > > Thank you, > Hannah > > > > > Re: [Freesurfer] Welch's t-test for HOV violation > 2019-03-13 Thread Greve, Douglas N.,Ph.D. > Hi Hannah, please include the previous correspondence so that we have context. > Also, please remember to post to the list and not to us personally. > thanks! > doug > > > > > On 3/13/19 10:52 PM, Hannah CK wrote: > > External Email - Use Caution > > Hi Dr. Greve, > > Thank you for this response. Can extracting the means be done at the > whole-brain level? If we get the means and variances for each group, I'm > assuming we would need to use ROIs. Could you please clarify whether it's > possible to extract means across the whole brain? > > Thank you, > Hannah > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > Re: [Freesurfer] Welch's t-test for HOV violation > 2019-03-11 Thread Greve, Douglas N.,Ph.D. > > > I used to have this about 20 years ago, but I stopped supporting it when it > did not fit cleanly into the GLM ... The shortest route is probably to do two > separate analyses with mri_glmfit, one for each group. This will output means > and variances for each group. Then use fscalc to compute maps of the Welch's > t. > > > On 3/11/19 1:28 PM, Hannah CK wrote: > > > > External Email - Use Caution > > > > We are conducting t-test comparisons across groups in which there is a > > large discrepancy in group sizes. HOV is violated. I've searched for > > ways to run Welch's t-test in FreeSurfer (or a similar analysis that > > does not assume homogeneity of variance) but am not finding one. > > > > Could anyone please advise on how to do this? > > > > Thank you. > >
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