Re: [Freesurfer] Problem with quantifyHAsubregions.sh

Dear Georgina, Can you please send me the list of files (a screenshot is also fine) inside the mri directory of any of your subjects, please? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of Georgina Angelopoulou Reply-To: Freesurfer support list Date:

[Freesurfer] Freesurfer TRACULA Error

External Email - Use Caution Hello FreeSurfer Developers, I am trying to apply TRACULA for the reconstruction of white matter pathways but I am getting an error when running the trac-all command which I haven’t managed to resolve. The TRACULA is applied on an MRI sample from

Re: [Freesurfer] PetSurfer - MG coregister

When you load it into freeview, use the aux/bbpet2anat.lta , eg, freeview orig.mgz aseg.mgz mgx.ctxgm.nii.gz:reg=aux/bbpet2anat.lta On 1/17/2023 12:46 PM, Marina Fernández wrote: External Email - Use Caution Dear experts, I am trying to do PVC on FBB-PET images using the following

Re: [Freesurfer] Dijk.m - Freesurfer Dijkstra MATLAB function

Hi Sarah, sorry, I don't know where that code came from; it is not being supported. Over the years, things find there way into FS, often from a postdoc or visiting fellow, then they leave and the program becomes orphaned. On 1/18/2023 5:31 PM, Sarah Lavelle wrote: External Email -

[Freesurfer] Multiple comparison correction

External Email - Use Caution Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: with three levels (d,m,h); gender (f, m), and two Nvariables So I can

Re: [Freesurfer] mri_segstats question: --avgwf for cross hemisphere ROI

Hi Bram, there is not a way to do it with a single command. You could use the aparc+aseg, merge the two hemi labels into one, then run mri_segstats. If you want to stick with pure surface-based analysis, then you'd have to  run mri_segstats twice, then just compute a weighted mean of the two

Re: [Freesurfer] freesufer

Try 1 -1 0 -1 1 0 ... 0 1 -1 0 -1 1 ... The first row look for the interaction between dm and fm, the second for mh and fm, then using both will test for an interaction in either On 1/16/2023 12:21 AM, David wrote: External Email - Use Caution Hi Freesurfer experts,     I'm very

Re: [Freesurfer] Quantification of regional volume using external atlas

You have to register the atlas to each individual person's space. You can do this with mri_coreg --mov atlas-template-brain.nii.gz --targ brain.mgz  --dof 12 --reg reg.lta Then map the atlas to the subject's space mri_vol2vol --mov atlas.nii.gz --targ brain.mgz --reg reg.lta --interp nearest

[Freesurfer] Problem with quantifyHAsubregions.sh

External Email - Use Caution Hello Freesurfer experts, I have accomplished hippocampal subfields segmentation using Freesurfer 7.3.2. However, I have trouble when I try to gather all volumes of all subjects in one single txt file. I type quantifyHAsubregions.sh hippoSf T1

Re: [Freesurfer] Two basic questions: brainmask file versions and qcache

Hello Emily, If it is to correct the wm/pial surfaces, I would refer you to these tutorials: * Pial surface edits: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview * White matter surface edits: