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