External Email - Use Caution
Hi Nick, I believe Doug had a similar problem (atlas not flipping for right hippocampus) because he mixed versions of FreeSurfer. Your call is definitely a bit weird… First, you’re running the hippocampal subfields with FS6. And then, you’re calling a script (segmentSubject.sh) which is supposedly segmenting the amygdala. Questions: 1. What’s inside that script (segmentSubject.sh)? 2. The amygdala module also segments the subfields. Why would you need to segment the subfields alone with FS6 in first place? Either way, the most likely solution is the following. Since the subjects have been run through recon-all (from what I can see), you can source the development version, and simply run: segmentHA_T1.sh bert (replace bert by your subject name). Further instructions, including commands to visualize the output, can be found here: http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Andrea, Nicolas" NANDREA@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 20 June 2018 at 21:09 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: "Jacobs, Heidi Irma Louisa" HJACOBS@mgh.harvard.edu Subject: [Freesurfer] Error with Hippocampal Subfields and Amygdala Nuclei
Hello,
I am attempting to run two FS commands to provide data on the hippocampal subfields and the amygdala nuclei. I have run this on ~700 cases, but a few seem to have an error with the segmentation (see attached images for examples). Here is the script that I’ve run that shows where the data is and is run on the specific subject whose images are attached. This was written as a csh script.
#Hippocampal subfields setenv SUBJECTS_DIR /autofs/space/rincewind_003/users/Amygdala/subjects source /usr/local/freesurfer/nmr-stable6-env recon-all -s HAB_133_FOK_2.1 -hippocampal-subfields-T1 -no-isrunning
#Amygdala nuclei cd /autofs/space/rincewind_003/users/Amygdala/hippoAmyg ./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR left ./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR right
If you have any insight on what might be going wrong with the segmentation, that would be most helpful. The recon-all.log is included.
Thanks! Nick
Hi Eugenio,
Thanks for the response. We noted the segmentHA_T1.sh script but weren’t able to get it running (perhaps you can let me know how to source the development version of FS and we can try it out). The segmentSubject.sh script seems to be something you shared with Heidi last year – we decided to use this as we weren’t able to run the segmentHA script.
Thanks, Nick
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 21, 2018 at 3:58 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu, "Jacobs, Heidi Irma Louisa" HJACOBS@mgh.harvard.edu Subject: Re: [Freesurfer] Error with Hippocampal Subfields and Amygdala Nuclei
External Email - Use Caution Hi Nick, I believe Doug had a similar problem (atlas not flipping for right hippocampus) because he mixed versions of FreeSurfer. Your call is definitely a bit weird… First, you’re running the hippocampal subfields with FS6. And then, you’re calling a script (segmentSubject.sh) which is supposedly segmenting the amygdala. Questions: 1. What’s inside that script (segmentSubject.sh)? 2. The amygdala module also segments the subfields. Why would you need to segment the subfields alone with FS6 in first place? Either way, the most likely solution is the following. Since the subjects have been run through recon-all (from what I can see), you can source the development version, and simply run: segmentHA_T1.sh bert (replace bert by your subject name). Further instructions, including commands to visualize the output, can be found here: http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Andrea, Nicolas" NANDREA@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 20 June 2018 at 21:09 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: "Jacobs, Heidi Irma Louisa" HJACOBS@mgh.harvard.edu Subject: [Freesurfer] Error with Hippocampal Subfields and Amygdala Nuclei
Hello,
I am attempting to run two FS commands to provide data on the hippocampal subfields and the amygdala nuclei. I have run this on ~700 cases, but a few seem to have an error with the segmentation (see attached images for examples). Here is the script that I’ve run that shows where the data is and is run on the specific subject whose images are attached. This was written as a csh script.
#Hippocampal subfields setenv SUBJECTS_DIR /autofs/space/rincewind_003/users/Amygdala/subjects source /usr/local/freesurfer/nmr-stable6-env recon-all -s HAB_133_FOK_2.1 -hippocampal-subfields-T1 -no-isrunning
#Amygdala nuclei cd /autofs/space/rincewind_003/users/Amygdala/hippoAmyg ./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR left ./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR right
If you have any insight on what might be going wrong with the segmentation, that would be most helpful. The recon-all.log is included.
Thanks! Nick
freesurfer@nmr.mgh.harvard.edu
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Andrea, Nicolas -
Iglesias Gonzalez, Eugenio