Okay, I changed some other things and now the recon-all is running. I will see how it looks tomorrow.
I used: recon-all -all \ > -i ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz -s new_trial_20110815 \ > -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ > -T2 ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \ > -T2pial -hippocampal-subfields-T1 Thanks! On Thu, Jul 7, 2016 at 2:15 PM, Vaz pandolfo, Renata <r...@njit.edu> wrote: > Thank you! > > But now the error is: > > ERROR: cannot find > o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz > 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 > > recon-all -s 20110815 exited with ERRORS at Do 7. Jul 14:14:09 CEST 2016 > > Maybe I have to put the whole path? > > On Thu, Jul 7, 2016 at 2:10 PM, Krieger, Donald N. <krieg...@upmc.edu> > wrote: > >> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >
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