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/HippocampalSubfieldsAndNucleiOfAmy...) on the development version of FreeSurfer. However, I am running into a couple errors when running the segmentHA_T1.sh script.
The first error is that the script is looking for segmentSubjectT1_autoEstimateAlveusML in the wrong directory. It is currently looking for this command in /usr/local/freesurfer/bin/ however I need to change this path to /g5/dcn/freesurfer_testing/HippoSegment_Test/freesurfer/bin/. I couldn't find where to change this path in run_segmentSubjectT1_autoEstimateAlveusML.sh. Where is this path defined so I can change it?
Secondly, the error output states that I am missing the following files in the subject's mri folder: lh.hippoSfVolumes-T1.v21.txt lh.amygNucVolumes-T1.v21.txt rh.hippoSfVolumes-T1.v21.txt rh.amygNucVolumes-T1.v21.txt I believe these files are created using recon-all -all -s [subjectname]. I ran this command before segmentHA_T1.sh using MPRAGE dicoms, and it seemed to have run without noticeable error, but these four files are still missing. How would I go about resolving this to create these files?
Thank you in advance for the help!
Best, CC
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Dear CC,
Did you source FreeSurfer at /g5/dcn/freesurfer_testing/HippoSegment_Test/freesurfer/ ?
setenv FREESURFER_HOME /g5/dcn/freesurfer_testing/HippoSegment_Test/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh
Cheers,
/Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Chen, Christine" ChenC@kennedykrieger.org Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 1 October 2019 at 10:10 To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Incorrect Path and Missing Files
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/HippocampalSubfieldsAndNucleiOfAmy...) on the development version of FreeSurfer. However, I am running into a couple errors when running the segmentHA_T1.sh script.
The first error is that the script is looking for segmentSubjectT1_autoEstimateAlveusML in the wrong directory. It is currently looking for this command in /usr/local/freesurfer/bin/ however I need to change this path to /g5/dcn/freesurfer_testing/HippoSegment_Test/freesurfer/bin/. I couldn’t find where to change this path in run_segmentSubjectT1_autoEstimateAlveusML.sh. Where is this path defined so I can change it?
Secondly, the error output states that I am missing the following files in the subject's mri folder: lh.hippoSfVolumes-T1.v21.txt lh.amygNucVolumes-T1.v21.txt rh.hippoSfVolumes-T1.v21.txt rh.amygNucVolumes-T1.v21.txt I believe these files are created using recon-all -all -s [subjectname]. I ran this command before segmentHA_T1.sh using MPRAGE dicoms, and it seemed to have run without noticeable error, but these four files are still missing. How would I go about resolving this to create these files?
Thank you in advance for the help!
Best, CC
________________________________ Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
freesurfer@nmr.mgh.harvard.edu
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Chen, Christine -
Iglesias Gonzalez, Juan E.