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. > >
_______________________________________________ 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.
