Hi Renata, Is there a problem with the “-s” argument, i.e. the “/” in - s 20110815/
HTH - Don From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Vaz pandolfo, Renata Sent: Thursday, July 07, 2016 8:05 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label Dear FreeSurfer developers, I am running recon-all on a healthy subject and I am also trying to get the hippocampal subfields segmentation. On the mri directory there is no hippocampus output, and the recon-all exited with errors. From my understanding, the error is with the lh.BA1_exvivo.label: SUBJECTS_DIR /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815 FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label The command I used was: recon-all -all \ -i ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz -s 20110815/ \ -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ -T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \ -T2pial -hippocampal-subfields-T1 When trying to solve the problem, I noticed that I could have run a separate command for the hippocampal subfields and I ran this one: recon-all \ -s 20110815/ \ -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ -hippocampal-subfields-T1T2 ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz 20110815_T2 Since the previous data had errors, I didn't really expect this to work, but I tried it anyways. It exited "without errors", but on the log there was the following error twice: Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf Extra info: Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611 uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux logs: recon-all and hippocampal-subfields-T1T2 attached If anyone has had the same problem, could you please tell me how to solve it? And if I am doing something wrong, please tell me the correct way so I can continue with the analysis. Thank you! Renata
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