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Thank you!
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: 23 June 2020 05:09
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] error in "recon-all -all -s subject
-hippocampal-subfields-T1": exited with errors
You have to run through all of recon-all before running the subfields, so just
add -all to the command line
On 6/22/2020 2:06 PM, Shimura, Yuki wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to compute calculate hippocampal volumes, as described on the
MultiModal FMRI tutorial "Segmentation of hippocampal
subfields"(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfields&data=02%7C01%7C%7C4dc7bebb5130470f0a0e08d81722d85c%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637284785714267348&sdata=oV04%2F6ukiC7SEvIPKO4Tb2%2BeZxYgO%2FED02ewMFdqlUE%3D&reserved=0>),
but I get the following error when I run the following command:
Command:
recon-all -s subject -hippocampal-subfields-T1
Error:
recon-all -s TNU_AIDAZ_3002_T1 exited with ERRORS at Mon Jun 22 15:42:08 JST
2020
(TNU_AIDAZ_3002_T1 is the subject name)
Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive
attached the recon-all.log in case it's of any use.
Here are few contexts:
a) I had the following command for recon-all for my subject:
recon-all -i ${SUBJECTS_DIR}/subject_structual_image_file.nii -s subject -all
-qcache -3T
b) this was done without an error
c) now I want to do "
recon-all -s subject -hippocampal-subfields-T1"
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform: CentOS release 6.7 (Final)
3) recon-all.log: see attached
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