[Freesurfer] Inconsistent Morphology Output

2019-11-08 Thread Chen, Christine
External Email - Use Caution Hello, My lab has been running T1 (MPRAGE) data through run_subject (uses recon-all, autorecon, mris_volume and mris_wm_volume) then through run.r (pulls freesurfer.r and pedbirn.r) using the Desikan-Killiany atlas to output measures of cortical mor

[Freesurfer] Hippocampal and Amygdala Segmentation Error - Incorrect Path and Missing Files

2019-10-01 Thread Chen, Christine
External Email - Use Caution To whom it may concern, I am attempting to run the hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) on the development version of FreeSurfer. However, I am running into a couple

[Freesurfer] Hippocampal and Amygdala Segmentation Error - Incorrect Path and Missing Files

2019-09-16 Thread Chen, Christine
External Email - Use Caution To whom it may concern, I am attempting to run the hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) on the development version of FreeSurfer. However, I am running into a couple

Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found

2019-07-26 Thread Chen, Christine
t; on behalf of "Chen, Christine" mailto:ch...@kennedykrieger.org>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, 26 July 2019 at 09:47 To: "'freesurfer@nmr.mgh.harvard.edu'" mailto:freesurfer@nmr.mgh.harvard.edu&

[Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found

2019-07-26 Thread Chen, Christine
External Email - Use Caution To whom it may concern, I am trying to run hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) on FreeSurfer v6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). I wa