Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc
I'm not sure if "mri_convert *junc.mnc* junk.mgh" was a typo, however, I tried both (junc.mnc, and junk.mnc), and there were errors on both. You're right, I got the same error (using junk.mnc). I'm going to downgrade and see if that helps. On Tue, Feb 7, 2017 at 7:43 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > It may be the version of minc you are using. On our system, we use version > 1.5, but it seems to work with 2.2. I don't have access to 2.3. Can you try > this > > mri_convert orig.mgz orig.nii > nii2mnc orig.nii junk.mnc > mri_convert junc.mnc junk.mgh > > I'm thinking that the last command will fail > > > On 2/7/17 6:27 PM, Muhammad Khan wrote: > > Thanks for getting back to me. > I ran that command from the $SUBJECTS_DIR/TEST01/mri folder and this is > the output: > > *-rw-rw-r-- 1 root 1590 31M Feb 7 10:14 >> ./tmp.mri_nu_correct.mni.30405/nu1.mnc* > > > I do have multiple disks mounted on the server, but they all have more > than enough space. The directory of the freesurfer folder has over 1.5TB. > Are any temporary folders created in a different location other than the > freesurfer directory? > > Thanks! > > > > On Tue, Feb 7, 2017 at 4:21 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> > wrote: > >> not sure what is going wrong here. For some reason mri_convert does not >> think that the mnc file is a minc file. Can you verify that you did not run >> out of space on that disk? Can you send the result of >> >> ls -l ./tmp.mri_nu_correct.mni.30405/nu1.mnc >> >> On 2/7/17 2:59 PM, Muhammad Khan wrote: >> >> >> >> >> Hi FreeSurfer Developers, >> >> I have been trying the 'recon-all -all -s TEST01' command, however I run >> into the following error: >> >> mri_convert ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz --like >>> orig.mgz --conform >>> mri_convert.bin ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz >>> --like orig.mgz --conform >>> ncopen: filename "./tmp.mri_nu_correct.mni.30405/nu1.mnc": Not a netCDF >>> file >>> miopen: MINC package entry point >>> Error opening ./tmp.mri_nu_correct.mni.30405/nu1.mnc >>> *mincRead(): error reading volume from file >>> ./tmp.mri_nu_correct.mni.30405/nu1.mnc* >>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ >>> reading from ./tmp.mri_nu_correct.mni.30405/nu1.mnc... >>> Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC >>> 2016 x86_64 x86_64 x86_64 GNU/Linux >>> recon-all -s TEST01 exited with ERRORS at Tue Feb 7 10:14:31 PST 2017 >>> For more details, see the log file /mnt/data/freesurfer/subjects/ >>> TEST01/scripts/recon-all.log >>> To report a problem, see http://surfer.nmr.mgh.harvard. >>> edu/fswiki/BugReporting >> >> >> I tried looking in the email-archives, although people had the same >> error, I wan unable to find a fix for it. My linux server is running on >> CentOS 6.8 and I am using the latest freesurfer release (v.6.0). >> >> These are the versions of some of the programs that are installed on the >> server: >> >>> charcot:~# mnc2nii -version >>> program: 2.3.01 >>> libminc: 2.3.01 >>> netcdf : 4.3.3 of Feb 8 2016 14:56:05 $ >>> HDF5 : 1.8.15 >> >> >> >> >> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0 >> 2) Platform: CentOS release 6.8 (Final) >> 3) uname -a: Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 >> 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux >> 4) recon-all.log: see attached >> >> I have also attached my recon-all log file. If there is anything else I >> can provide, please let me know. >> Thanks, >> Muhammad >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ___ Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e >> du/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
Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc
Thanks for getting back to me. I ran that command from the $SUBJECTS_DIR/TEST01/mri folder and this is the output: *-rw-rw-r-- 1 root 1590 31M Feb 7 10:14 > ./tmp.mri_nu_correct.mni.30405/nu1.mnc* I do have multiple disks mounted on the server, but they all have more than enough space. The directory of the freesurfer folder has over 1.5TB. Are any temporary folders created in a different location other than the freesurfer directory? Thanks! On Tue, Feb 7, 2017 at 4:21 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > not sure what is going wrong here. For some reason mri_convert does not > think that the mnc file is a minc file. Can you verify that you did not run > out of space on that disk? Can you send the result of > > ls -l ./tmp.mri_nu_correct.mni.30405/nu1.mnc > > On 2/7/17 2:59 PM, Muhammad Khan wrote: > > > > > Hi FreeSurfer Developers, > > I have been trying the 'recon-all -all -s TEST01' command, however I run > into the following error: > > mri_convert ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz --like >> orig.mgz --conform >> mri_convert.bin ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz >> --like orig.mgz --conform >> ncopen: filename "./tmp.mri_nu_correct.mni.30405/nu1.mnc": Not a netCDF >> file >> miopen: MINC package entry point >> Error opening ./tmp.mri_nu_correct.mni.30405/nu1.mnc >> *mincRead(): error reading volume from file >> ./tmp.mri_nu_correct.mni.30405/nu1.mnc* >> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ >> reading from ./tmp.mri_nu_correct.mni.30405/nu1.mnc... >> Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC >> 2016 x86_64 x86_64 x86_64 GNU/Linux >> recon-all -s TEST01 exited with ERRORS at Tue Feb 7 10:14:31 PST 2017 >> For more details, see the log file /mnt/data/freesurfer/subjects/ >> TEST01/scripts/recon-all.log >> To report a problem, see http://surfer.nmr.mgh.harvard. >> edu/fswiki/BugReporting > > > I tried looking in the email-archives, although people had the same error, > I wan unable to find a fix for it. My linux server is running on CentOS 6.8 > and I am using the latest freesurfer release (v.6.0). > > These are the versions of some of the programs that are installed on the > server: > >> charcot:~# mnc2nii -version >> program: 2.3.01 >> libminc: 2.3.01 >> netcdf : 4.3.3 of Feb 8 2016 14:56:05 $ >> HDF5 : 1.8.15 > > > > > 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0 > 2) Platform: CentOS release 6.8 (Final) > 3) uname -a: Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 > 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux > 4) recon-all.log: see attached > > I have also attached my recon-all log file. If there is anything else I > can provide, please let me know. > > Thanks, > Muhammad > > > > > > > > > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > 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.
