[Freesurfer] mris_make_average_surface, flirt transformations question

External Email - Use Caution Freesurfer experts, I'm trying to make average surfaces for a collection of subjects into a template space. I have performed the following flirt registration per subject: flirt -in $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz -ref template0.nii.gz -omat $

[Freesurfer] Question about sclimbic

External Email - Use Caution I receive an error when I try to run the sclimbic module, do you have any suggestions on why this might be happening? : Loaded input image from /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/GP1462~1/mri/nu.mgz Traceback (most recent call last): File

[Freesurfer] Password for unzipping of VM

External Email - Use Caution Dear FreeSurfer experts, I would like to unzipp the VM in order to run FreeSurfer on windows. Could you provide me the password for unzipping? Thank you very much in advance, best regards, Malina ___ Freesur

[Freesurfer] FreeSurfer Password

External Email - Use Caution Hi, my name us José Carlos López Mata. I'm a biomedical engineering at Universidad Autonoma Metropolitana in Mexico City. I'm working with fMRi images and i need to use Freesurfer for my project so, i request de activation password, please. ___

[Freesurfer] NoPVC PET

External Email - Use Caution Dear experts, I would like to get a noPVC PET volume scaled by the intensity of the pons, then project it and apply standard surface-based analysis. On the PetSurfer website it says: ** If you do not want to perform PVC, you can just run mri_gtmpvc

[Freesurfer] mri_vol2surf, error: mghRead(/mri/orig.mgz, -1)

External Email - Use Caution Hello, I am trying to map tumour+oedema lesion masks (generated with ITKSnap) to subjects' freesurfer surface (in native space) using mri_vol2surf. This is an example of the command I am using for a specific subject: mri_vol2surf --mov CI_01_t+oedem

[Freesurfer] Cutting an occipital patch

External Email - Use Caution Hello, I need to cut the occipital pole in order to make a retinotopy analysis. I read that tksurfer no more exists, and with freeview I only succeed in cutting the plane but I'm having trouble with separating it into a patch with the occipital part onl