Dear Zeke, This is the output:
"Mon Feb 22 18:27:05 CET 2016 /usr/local/freesurfer/subjects/myscan /usr/local/freesurfer/bin/recon-all -s myscan -i myscan.nii.gz subjid myscan setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0 Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15308 maxlocks unlimited maxsignal 15308 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buffers cached Mem: 3940392 3452568 487824 223760 262988 2343920 -/+ buffers/cache: 845660 3094732 Swap: 2023420 77288 1946132
######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /usr/local/freesurfer/subjects/myscan
mri_convert /usr/local/freesurfer/subjects/myscan.nii.gz /usr/local/freesurfer/subjects/myscan/mri/orig/001.mgz
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s myscan exited with ERRORS at Mon Feb 22 18:27:07 CET 2016
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" It creates the directory myscan but the folders myscan/mri/orig and myscan/mri/transforms are empty. Before running I changed the rights -R a+w for /usr/local/freesurfer/subjects.
I tried to use mri_convert myscan.nii.gz myscan.mgz and it doesn't do anything, no error message it just skips to a new line. mri_convert -h or mri_convert --help also don't have any output. And recon-all -s bert -autorecon1 gives:
"Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwxrwx 1 root root 472994 Feb 8 16:54 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /space/freesurfer/centos4.0/stable #-------------------------------------------- #@# MotionCor Mon Feb 22 18:24:35 CET 2016 Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Mon Feb 22 18:24:35 CET 2016"
I tried to use
If I try to run:
"freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red" as indicated on the website nothing happens, no error message.
-----Origineel Bericht-----
Van: freesurfer-request@nmr.mgh.harvard.edu Aan: freesurfer@nmr.mgh.harvard.edu Datum: 10-02-2016 17:28 Onderwerp: Freesurfer Digest, Vol 144, Issue 14
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Today's Topics:
2. Re: mri_convert Ubuntu 14.04 LTS not working (neither is freeview) (Z K)
Message: 2 Date: Tue, 9 Feb 2016 12:55:18 -0500 From: Z K zkaufman@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 56BA2806.6060106@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed
I just did a tst of mri_convert of freesurfer v5.3 on my Ubuntu 14.04 machine and it ran successfully. Freeview also ran (after typing the libjpeg symlink command).
Can you provide any error or terminal output information?
-Zeke
On 02/08/2016 12:41 PM, Veronica.Popescu wrote:
Dear all, I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit). The mri_convert doesn't work with no error message. which mri_convert gives /usr/local/freesurfer/bin/mri_convert. Of course neither does recon-all (which exits with errors with no error message in the log). I made sure all the paths are 777. I did the recommended "sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3" in x86_64-linux-gnu. The same problem with freeview, nothing happens. Thank you in advance! Veronica
End of Freesurfer Digest, Vol 144, Issue 14
-- Revalidatie & MS Centrum VZW | Overpelt Boemerangstraat 2 B-3900 Overpelt Tel.: 011 / 809 100 Fax: 011 / 66 28 86 http://www.msreva.be info@msreva.be
Disclaimer: http://www.msreva.be/default.aspx?main
I suspect its failing because the data file is zipped. Try unzipping it first, then run the recon:
$> gunzip myscan.nii.gz $> /usr/local/freesurfer/bin/recon-all -s myscan -i myscan.nii.gz
If that does not work please upload the data and I will take a look.
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
-Zeke
On 02/22/2016 12:43 PM, Veronica.Popescu wrote:
Dear Zeke, This is the output:
"Mon Feb 22 18:27:05 CET 2016 /usr/local/freesurfer/subjects/myscan /usr/local/freesurfer/bin/recon-all -s myscan -i myscan.nii.gz subjid myscan setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0 Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15308 maxlocks unlimited maxsignal 15308 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buffers cachedMem: 3940392 3452568 487824 223760 262988 2343920 -/+ buffers/cache: 845660 3094732 Swap: 2023420 77288 1946132
######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /usr/local/freesurfer/subjects/myscan
mri_convert /usr/local/freesurfer/subjects/myscan.nii.gz /usr/local/freesurfer/subjects/myscan/mri/orig/001.mgz
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s myscan exited with ERRORS at Mon Feb 22 18:27:07 CET 2016
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" It creates the directory myscan but the folders myscan/mri/orig and myscan/mri/transforms are empty. Before running I changed the rights -R a+w for /usr/local/freesurfer/subjects.
I tried to use mri_convert myscan.nii.gz myscan.mgz and it doesn't do anything, no error message it just skips to a new line. mri_convert -h or mri_convert --help also don't have any output. And recon-all -s bert -autorecon1 gives:
"Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwxrwx 1 root root 472994 Feb 8 16:54 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /space/freesurfer/centos4.0/stable #-------------------------------------------- #@# MotionCor Mon Feb 22 18:24:35 CET 2016 Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Mon Feb 22 18:24:35 CET 2016"
I tried to use
If I try to run:
"freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red" as indicated on the website nothing happens, no error message.
-----Origineel Bericht-----
Van: freesurfer-request@nmr.mgh.harvard.edu Aan: freesurfer@nmr.mgh.harvard.edu Datum: 10-02-2016 17:28 Onderwerp: Freesurfer Digest, Vol 144, Issue 14
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
2. Re: mri_convert Ubuntu 14.04 LTS not working (neither is freeview) (Z K)
Message: 2 Date: Tue, 9 Feb 2016 12:55:18 -0500 From: Z K zkaufman@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 56BA2806.6060106@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed
I just did a tst of mri_convert of freesurfer v5.3 on my Ubuntu 14.04 machine and it ran successfully. Freeview also ran (after typing the libjpeg symlink command).
Can you provide any error or terminal output information?
-Zeke
On 02/08/2016 12:41 PM, Veronica.Popescu wrote:
Dear all, I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit). The mri_convert doesn't work with no error message. which mri_convert gives /usr/local/freesurfer/bin/mri_convert. Of course neither does recon-all (which exits with errors with no error message in the log). I made sure all the paths are 777. I did the recommended "sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3" in x86_64-linux-gnu. The same problem with freeview, nothing happens. Thank you in advance! Veronica
End of Freesurfer Digest, Vol 144, Issue 14
-- Revalidatie & MS Centrum VZW | Overpelt Boemerangstraat 2 B-3900 Overpelt Tel.: 011 / 809 100 Fax: 011 / 66 28 86 http://www.msreva.be info@msreva.be
Disclaimer: http://www.msreva.be/default.aspx?main
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Z K