Re: [Freesurfer] PETSurfer: Equivalence between surfaces un gtmseg space and native surface?

External Email - Use Caution Ok so if I well understand surface in the gtmseg space would not have finer resolution than surface in native space (big voxel)? On 06/03/2019 23:48, Greve, Douglas N.,Ph.D. wrote: > I don't think so. The surfaces are at about 1mm resolution, which sh

Re: [Freesurfer] Resampling a gifti image to nifti using mri_surf2vol fails

External Email - Use Caution Hi, First I tried to use my original mask which is a gifti with a single darray as NIFTI_INTENT_ESTIMATE that contains 0 or 1 for each vertex. But I got it: " ** DA[0] has coordsys with intent NIFTI_INTENT_ESTIMATE (should be NIFTI_INTENT_POINTSET

Re: [Freesurfer] Resampling a gifti image to nifti using mri_surf2vol fails

Hi Bastien can you send us the full command lines and screen output of whatever you have run? cheers Bruce On Thu, 7 Mar 2019, CAGNA Bastien wrote: External Email - Use Caution Hi, First I tried to use my original mask which is a gifti with a single darray as NIFTI_INTENT

Re: [Freesurfer] Creating Labels

Try mri_surfcluster On 3/6/19 10:03 PM, Jahan, Bushra wrote: > Hello, > > I am wondering how to generate a label in FreeSurfer from peak > activation in a cluster - is there a specific command? > > Thank you. > > ___ > Freesurfer mailing list > Freesurf

Re: [Freesurfer] PETSurfer: Equivalence between surfaces un gtmseg space and native surface?

The surface resolution is set during the recon-all analysis and is uninfluenced by the PET data On 3/7/19 3:16 AM, Matthieu VANHOUTTE wrote: > External Email - Use Caution > > Ok so if I well understand surface in the gtmseg space would not have > finer resolution than surface in native

Re: [Freesurfer] projfrac question

Hi Doug Thank you very much for your reply. I ran one of my subjects with the command below and I got this error: preproc-sess.test -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface fsaverage lhrh -fsd bold -d $dir/all_subjects -force Does it mean I should run it with expert option flag

Re: [Freesurfer] Gray matter segmentation

External Email - Use Caution Hi Greve, I uploaded my data to the ftp site, Thanks, Maxime De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Greve, Douglas N.,Ph.D. Envoyé : 6 mars 2019 18:26 À : freesurfer@nmr.mgh.harvard.edu

[Freesurfer] regions of Yeo 17 networks in fast

External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering). in FS-FAST. Which is the command line to be used to create a segmentation

Re: [Freesurfer] Accounting for family relation in FS

Sorry for the delay ... This looks like a fairly complicated design, and I'm not sure how to think about it. What do you actually want to test in the end? BTW, the FSGD file you have there will not work. The variables are for continuous variables (eg, age) and not discrete variables (eg, sex or

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

External Email - Use Caution Hi Doug, I realized this error a couple of days ago and now it works. Thank you, Arsenije ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu

Re: [Freesurfer] regions of Yeo 17 networks in fast

You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM,

Re: [Freesurfer] projfrac question

Can you try it again? this time use -projfrac 0.2 pf020  (ie, add "pf020" after 0.2). Then when you use mkanalysis-sesss, add -expkey pf020 to the command line. The pf020 will be included in the output file name to make it unique. This allows you to use a single project folder (ie, you don't ne

Re: [Freesurfer] Extraction of anatomical locations using Matlab

Can you include the previous emails so we have context? On 3/7/19 6:16 PM, Sparsh Jain wrote: > > External Email - Use Caution > > Good evening. >  Thanks a lot for the help. It worked ! > While most of the labels were correct, the matlab script returned the > wrong location for one point

Re: [Freesurfer] Extracting anatomical locations for a set of RAS coordinates

Is that point labeled as WM in the aseg? If so, then it is not a problem with matlab:) On 3/7/19 5:58 PM, Sparsh Jain wrote: > > External Email - Use Caution > > Thanks a lot! It worked. > While most of the labels were correct, the matlab script returned the > wrong location for one poin

Re: [Freesurfer] Extracting anatomical locations for a set of RAS coordinates

External Email - Use Caution I see. How may I check that? Sparsh On Thu, Mar 7, 2019 at 6:42 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Is that point labeled as WM in the aseg? If so, then it is not a problem > with matlab:) > > On 3/7/19 5:58 PM, Sparsh Jain

[Freesurfer] mri_glmfit-sim cluster correction threshold inquiry

External Email - Use Caution Hello, I am planning on running a correction for multiple comparisons, and I was hoping to use a vertex wise cluster forming threshold of 1.3, however after reading more when I ran the mri_glmfit-sim —help command it recommends using the permutation