Re: [Freesurfer] Calculating gray matter volume and BPF from Samseg output

External Email - Use Caution Hi Maaike I think the easiest way is to use the fspython interpreter included in FreeSurfer. If you put the lines below in a text file called "sum_volumes.py" and do "fspython sum_volumes.py" in the samseg results directory (the directory where the fil

Re: [Freesurfer] mri_easyreg

External Email - Use Caution Hello, so the command I used is: mri_easyreg --ref MP2RAGE_uni_resampled_2mm.nii.gz --flo sub017_ute_anat.nii.gz --ref_seg mprage_seg.nii --flo_seg ute_seg.nii The output I get is: Illegal instruction I also tried putting the absolute path to the file

[Freesurfer] How to change mri_convert --conform to use another flag while running recon-all

External Email - Use Caution Dear Freesurfer support team, I noticed that the interpolation setting used within the first few steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is reducing the data quality for data that has a rectangular field of view. I need to

Re: [Freesurfer] mri_easyreg

External Email - Use Caution  When you setup the freesurfer 7.4.1 environment from the terminal, check you see the output below when running bash shell from the terminal.  If you see all the same output, then it should at least work to get the help info from the command… $ bash