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"

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.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer