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), 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
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), 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"
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Platform: CentOS release 6.7 (Final)
- recon-all.log: see attached
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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/HippocampalSubfieldshttps://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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7C%7C4dc7bebb5130470f0a0e08d81722d85c%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637284785714277352&sdata=KZ%2B9%2B%2FzfvD5GYRnOrw13MViFXMfe%2ByTBFxAOyRDXZRM%3D&reserved=0
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Shimura, Yuki