[Freesurfer] Brodmann area parcellation

External Email - Use Caution Dear Freesurfer Developers, I am trying to get the seed mask of premotor and motor cortex. Because I can't get it through 'recon-all -all', I tried to find brodmann area ('recon-all -s subjid -ba-labels') But I received ERROR message. Can you tell me

Re: [Freesurfer] question about aparcstats2table

External Email - Use Caution Hi, I use the attached script to utilize aparcstats2table. This will generate surface, thickness, thickness_SD, and volume csv files. Hope this helps. Kiyotaka External Email - Use Caution > > Hi FreeSurfer experts, > I want to converts a co

[Freesurfer] Vertex by Vertex Analysis

External Email - Use Caution Hello, I would like to perform a group difference analysis with gray-white matter contrast between healthy controls and patients, covarying for the cortical thickness at each vertex throughout the entire brain surface. How would we go about doing this?

Re: [Freesurfer] Segmentation faule recon-all

Did you check the talairach transform? See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview On 10/4/2019 1:37 PM, Backhausen, Lea wrote: External Email - Use Caution Dear FreeSurfer experts, when running the recon -all –all command (I included the -3T flag) with

Re: [Freesurfer] ERROR gtmseg

That is kind of weird. It says it has found a segmentation with number 229, but we don't have that code in our system. Can you find the 229 voxels in the aparc+aseg.mgz? On 10/4/2019 6:28 PM, Marina Fernández wrote: External Email - Use Caution Dear experts, The following error occurs

Re: [Freesurfer] Question on Z-scoring

That looks correct to me On 10/4/2019 5:39 PM, Nillo, Ryan Michael R wrote: Hello FreeSurfer users/devs, I have a question on z-scoring. I would like to produce z-scored volume maps for each subject in my study. Is my process correct? 1) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $su

[Freesurfer] ERROR gtmseg

External Email - Use Caution Dear experts, The following error occurs with one subject when I am running gtmseg command: *Computing colortable* *ERROR: cannot find match for subcortical segid 229* *ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas apas+head.mgz --no

[Freesurfer] Question on Z-scoring

Hello FreeSurfer users/devs, I have a question on z-scoring. I would like to produce z-scored volume maps for each subject in my study. Is my process correct? 1) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $sub/surf/$h.volume —tval $sub/surf/$h.volume.mgh —sfmt curv (convert .volume f

Re: [Freesurfer] Tracula

Hi Juan - You can see usage info for dt_recon if you run it without arguments: USAGE: dt_recon Required Aruments: --i invol --b bvals bvecs --s subjectid --o outputdir ... So --b takes both bvals and bvecs one after the other, and --s is the subject name as found under $SUBJECTS_DIR

[Freesurfer] Tracula

External Email - Use Caution Hi, I am trying to make the recon with diffusion images for running tracula. I gave this command: set cmd = dt_recon set cmd = ($cmd --b $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvals set cmd = ($c

Re: [Freesurfer] Curvature estimation from Hessian

External Email - Use Caution Hi Bruce, thank you for your explanation. I think I might have an idea, why the Hessian matrix works in this case, maybe you can confirm or correct me if I'm wrong. Usually, if you're having a 2d surface in space, the principle curvatures are the ei

Re: [Freesurfer] Exporting ROI segmentation in T1 DICOM header

External Email - Use Caution Dear both, many thanks for your replies. I will try both options and see what happens. Best, Vânia de Aguiar, PhD Assistant Professor in Neurolinguistics University of Groningen Faculty of Arts Oude Kijk in 't Jatstraat 26 Room 1315.0408 9712 EK, Gro

[Freesurfer] Label created in the symmetric space

External Email - Use Caution Dear Freesurfer Experts, I would appreciate your help. I will explain first what I have done and where my problem is. I want to measure the cortical thickness in stroke patients. Therefore I followed Douglas' instructions provided in this link