Re: [Freesurfer] recon-all , fsaverage ?

Hi, Your $SUBJECTS_DIR should be pointed to the directory where your subjects' data live. To symlink your $SUBJECTS_DIR to $FREESURFER_HOME/subjects/fsaverage be sure to have sourced FREESURFER, set your SUBJECTS_DIR, then cd $SUBJECTS_DIR

[Freesurfer] aseg stats on 001.mgz

External Email - Use Caution Hi, I can't seem to figure out the best way to load the aseg and the raw mgz file in the same space. Is there a registration file somewhere that I can use for that. I can see that FreeView can see this, but I am having trouble figuring out the right wa

Re: [Freesurfer] almost empty mask.mgh with glmfit

External Email - Use Caution Hi Doug, Thanks. Yeah I am sure. I went through all my subjects with the time button. Could it potentially be an internal rounding issue (almost all my pet values are between 0 and 1, so they are put to 0?) Most likely not, but still not sure what's ha

Re: [Freesurfer] almost empty mask.mgh with glmfit

Are you sure that there is not one subject that has a bunch of 0s? All it would take is one. You can also look at a "time course" of your subjects by clicking on the time course button in freeview On 1/14/2021 11:38 AM, Julie Ottoy wrote: External Email - Use Caution Hi Doug, thank y

Re: [Freesurfer] FW: Missing transformation files in longitudinal pipeline

Are you looking in the base/mri/transforms folder? If it is not there, can you send the recon-all.log file for the base run On 1/14/2021 11:12 AM, Nederpelt, D. van (David) wrote: External Email - Use Caution Hi FS-team, I ran a longitudinal recon-all stream(FS version 7.1.1)  and tr

Re: [Freesurfer] Qdec crash while analysis almost finished

External Email - Use Caution Hi Douglas, I used to work with v5.3(centOS6) before and recently I changed a new computer, so I hope to keep using the same version(v5.3) in case of some version problem with old results. But I couldn't perform a qdec analysis because It kept giving