FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc
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
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 <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
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
- 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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 greve@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
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
- Platform: CentOS release 6.8 (Final)
- 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
- 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 listFreesurfer@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.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <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 list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
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 greve@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 greve@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
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
- Platform: CentOS release 6.8 (Final)
- 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
- 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 listFreesurfer@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 of the e-mail.
Freesurfer mailing listFreesurfer@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@nmr.mgh.harvard.edu
-
Douglas Greve -
Muhammad Khan