Re: [Freesurfer] Freesurfer license

Thank you Paul, I am using fmriprep-32.1.4.simg, and built it using this command: singularity build ./fmriprep-23.1.4.simg docker://nipreps/fmriprep:23.1.4 I use this command to run fMRIprep: singularity run --nv --cleanenv -B -B -B -B -w --output-spaces {MNI152NLin2009cAsym:res-1,T1w:r

[Freesurfer] fmriprep and freesurfer license

External Email - Use Caution I use this on our HPC: apptainer run --cleanenv --bind ${MRIS}/data:/data:ro --bind ${MRIS}/derivatives/fmriprep:/outputs --bind ${MRIS}/fmriprep_work:/work ${APP} /data /outputs participant --participant_label ${Subject} --fs-license-file ${HOME}/

Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

If it is only one subject and you have no continuous variables, you can do it that way. If you have continuous variables, you will need to use DOSS (different-offset same slope) to force the slopes to be the same across classes (because you can't compute a slope from a single data point) On 5/

Re: [Freesurfer] Recon-all for a common template

Why did you do an lr reversal if it looked good? And when you say it looks good, what do you mean. One thing to double check is that the orientation looks ok. Load it in freeview. Up at the top you will see little brain images in coronal, sagital, and axial. When you click on one of those, the

Re: [Freesurfer] How to get the parcellations to the initial space as before running recon all

Does this web site https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat cover what you need to do? On 6/3/2024 10:58 AM, Reji, A. (Amal, Student M-EE) wrote: External Email - Use Caution Hi,     I was trying to get the mesh files for cortical parcellations after running re

Re: [Freesurfer] Freesurfer license

Hi Liz, What fmriprep container are you using and what are the full commands that are not working? Are you bind-mounting the freesurfer license file into the container via `singularity exec --bind`? -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] Freesurfer license

Hi, I am using singularity to run fmriprep, and it seems that it is not recognizing the location of my freesurfer license ( it is a new license). I have tried all three options for location, and none work: ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an ex

[Freesurfer] How to get the parcellations to the initial space as before running recon all

External Email - Use Caution Hi, I was trying to get the mesh files for cortical parcellations after running recon all. I used the Ernie data set which is the example dataset given by SimNIBS. I did recon all to the