[Freesurfer] lesions

Lots of questions about lesions: 1) What is the best way to measure the size of a lesion in Freesurfer? Or should it be drawn in afni and transported to Freesurfer somehow? 2) What is the best way to measure how much of each ROI is affected by the lesion? 3) Line 25 lists "Left-lesion" and

Re: [Freesurfer] Recon-all -i ... command does not create all 10 folders

You can try executing it with the -dontrun option doug Juergen Haenggi wrote: Dear Freesurfer users we are running Freesurfer 3.0.4 on a supercomputer. the problem is that the first recon-all command (recon-all -i ...) do not create all 10 folders per subjects, so that Freesurfer crashed w

Re: [Freesurfer] Recon-all -i ... command does not create all 10 folders

Hi Juergen, you can use -noaseg and only do one hemisphere (-hemi lh) which should make it quite a bit faster, but of course it won't work as well without the aseg. Did you check the recon-all.log to see if it had errors making directories? Although it should have aborted then. cheers, Bruce

[Freesurfer] Recon-all -i ... command does not create all 10 folders

Dear Freesurfer users we are running Freesurfer 3.0.4 on a supercomputer. the problem is that the first recon-all command (recon-all -i ...) do not create all 10 folders per subjects, so that Freesurfer crashed when trying to write lh.aparc.annot, because there is no folder called label. We then