Hi Anup I suspect the problem is choosing a subject with ".mgz" in the ID. I wouldn't include any of ".nii" ".mgz" or ".mgh" in a subject ID. Try rerunning and just using fsMM
cheers Bruce On Wed, 14 Jun 2017, Anup Bidesi wrote: > > Hello FreeSurfer Users, > > New to Freesurfer, I'm attempting to recon-all using : > > recon-all -all -i T1.nii -s op.nii.mgz (Attached recon-all log) > > The automated process begins normally and seems to run Autorecon Prrocessing > Stages 1-25, but at step 26 > (I think) and then exits with Error, per log as seen below: > > ------------------------------------------------------------- > > mghRead(/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.th > ickness, > -1): could not open file. > Filename extension must be .mgh, .mgh.gz > or .mgz > > ------------------------------------------------------------- > > Within the subject .mgz folder in Surf there was a tmp.pctsurfcon.14807 fold > er with > a file named lh.wm.mgh (size 569 kb). > > I ran this process a couple of times and the autorecon process would exit at > same step.I > tried looking up the Archive for any similar previous error messages but did > not find any. > Please advise. > > 1) FreeSurfer version: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > 2) Platform: Ubuntu 14.04 > > 3) uname -a: Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic > #164-Ubuntu > SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > 4) recon-all.log: see attached > > Thanks for your help, > > Anup > > _______________________________________________ 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.
