Can you send a command line and terminal output with the error? On 8/14/19 9:38 AM, Daliah Ross wrote: > > External Email - Use Caution > > Hello, > > I have tried using just one of the arguments, but I'm still not > getting my desired output. I'm not sure if I've explained my question > correctly. I am looking to get anatomical labels on the clusters that > I've already created through mri_surfcluster to find out where in the > cortex each cluster is. How would I go about doing this? I was hoping > that mri_segstats could give an output where it lists each cluster > starting with the biggest and where it is located. I've been able to > get this list, but without anatomical labels. I appreciate your help! > > Thank you, > Daliah > > *Daliah Ross* | [email protected] <mailto:[email protected]> > > Ph.D. Student, Clinical Psychology with Health Emphasis > Ferkauf Graduate School of Psychology > Yeshiva University > Albert Einstein College of Medicine > > > On Thu, Aug 8, 2019 at 8:01 PM Daliah Ross <[email protected] > <mailto:[email protected]>> wrote: > > Hi, > > No, we primarily wanted this for the un-permuted case, to be able > to identify the anatomical regions for each cluster. In addition, > we have thought about looking at the spatial cluster distribution > for the permutations to see if there are any regions which are > more prone to false positives, which might be indicative of e.g. > parcellation or imaging issues, but we haven’t yet figured out how > to best go about that step. And, yes, for the permutations we are > running mri_surfcluster and extracting the max cluster size per > permutation. Thank you for the advice! > > Daliah > > *Daliah Ross* | [email protected] <mailto:[email protected]> > > Ph.D. Student, Clinical Psychology with Health Emphasis > Ferkauf Graduate School of Psychology > Yeshiva University > Albert Einstein College of Medicine > > > On Wed, Aug 7, 2019 at 4:51 PM Greve, Douglas N.,Ph.D. > <[email protected] <mailto:[email protected]>> wrote: > > 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* | [email protected] > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>> > > > > Ph.D. Student, Clinical Psychology with Health Emphasis > > Ferkauf Graduate School of Psychology > > Yeshiva University > > Albert Einstein College of Medicine > > > > From: [email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>> > > <[email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>>> On Behalf Of > > Greve, Douglas N.,Ph.D. > > Sent: Tuesday, August 6, 2019 12:56 PM > > To: [email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>> > > 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* | [email protected] > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>> > > <mailto:[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> > > > > > > Ph.D. Student, Clinical Psychology with Health > Emphasis Ferkauf > > > Graduate School of Psychology Yeshiva University > Albert Einstein > > > College of Medicine > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > [email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>> > > > https://mail > > > .nmr.mgh.harvard.edu <http://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> > > > <http://40einstein.yu.edu>%7Cfde693609070412c457808d71a8f16f2% > > > > > > > 7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637007074183066654&sd > > > > ata=ALndUpHJ%2BYhuMzChviSn9ygf8H112mUKvVmJktGoqB4%3D&reserved=0 > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > > > > 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 > > > > > > 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. >
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