You should only pass one of --seg, --annot, or --slabel to mri_segstats. I don't understand how you are trying to use this in the context of your permutation. Is this something that you are running on each iteration? If so, it is probably not what you want to do. Probably you want to run mri_surfcluster to get the cluster sizes out.
On 8/7/19 1:31 PM, Daliah Ross wrote: > > External Email - Use Caution > > This is the command line: > mri_segstats --seg F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.mgh > --annot lh.aparc.annot lh parc --slabel fsaverage lh cortex --sum > F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.txt > > We are running the permutations within FS, but because our model is a > linear mixed model, and we didn't think that this would be compatible > with fspalm. So, we are running the permutations "manually" (i.e. we > are generating the random permutations, which in our case is just > switching the subject labels for the thickness data. We are then using > mri_surfcluster to extract the maximum cluster size per permutation > and will use the permutation distribution to determine our the > statistical significance of our results). In addition, our analyses > are a bit out of the ordinary in that the thickness data are an > independent variable in our model, for which we have a repeated > non-imaging measure as the outcome. Effectively, we are using the > thickness maps to generate vertex-wise regressors, with a fixed > outcome measure (fixed in the sense that it doesn't vary across the > brain). > > If you have any thoughts about how we could use fspalm in our case, > your advice would be most appreciated. > > Thanks again, > Daliah > > *Daliah Ross* | dro...@mail.yu.edu <mailto:dro...@mail.yu.edu> > > Ph.D. Student, Clinical Psychology with Health Emphasis > Ferkauf Graduate School of Psychology > Yeshiva University > Albert Einstein College of Medicine > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of > Greve, Douglas N.,Ph.D. > Sent: Tuesday, August 6, 2019 12:56 PM > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Help with MRI segstats > > Can you send command lines? Also, are you using the built-in > permutation tool or trying to do something outside of FS? > > On 8/6/19 8:40 AM, Daliah Ross wrote: > > > > External Email - Use Caution > > > > Hi FreeSurfer experts, > > > > I have a couple of questions regarding mri_segstats tool for an > > analysis on vertex-wise cortical thickness data. We are > attempting to > > compare maximum cluster sizes among permutations. We are having > > trouble figuring out how to get the anatomical label for each > cluster > > using the --slabel argument. We are also wondering if the > difference > > between cluster sizes between mri_surfcluster and mri_segstats > is due > > to partial volumes, and if so, how to correctly use the --pv > argument. > > It suggests in the wiki page that mri/norm.mgz volume is usually > used > > but I believe we need something surface-based since we are using > > thickness data. > > > > Thank you in advance for any help you can provide. > > > > Best, > > Daliah > > > > *Daliah Ross* | dro...@mail.yu.edu <mailto:dro...@mail.yu.edu> > <mailto:dro...@mail.yu.edu <mailto:dro...@mail.yu.edu>> > > > > Ph.D. Student, Clinical Psychology with Health Emphasis Ferkauf > > Graduate School of Psychology Yeshiva University Albert Einstein > > College of Medicine > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail > > .nmr.mgh.harvard.edu > > <http://nmr.mgh.harvard.edu>%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C0 > > 1%7Cmark.wagshul%40einstein.yu.edu > <http://40einstein.yu.edu>%7Cfde693609070412c457808d71a8f16f2% > > > 7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637007074183066654&sd > > ata=ALndUpHJ%2BYhuMzChviSn9ygf8H112mUKvVmJktGoqB4%3D&reserved=0 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cdross3%40mail.yu.edu%7Cdbb41053267d448fe28008d71b4187d2%7C04c70eb48f2648079934e02e89266ad0%7C1%7C1%7C637007840572533331&sdata=yKzDT4u1esPzure5GZ6MdKjG1fYemJGbV6dUkW3V45Y%3D&reserved=0 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
