Dear FreeSurfers,
I am new to FreeSurfer and just trying to run some simple volumetric analysis and I get a "Protocol error".
I went to look at the log file and it is 30 gigabytes in size so something is going awry here...
Is there a way to break this error down further to understand what may be going wrong?
I am running FreeSurfer in the Oracle virtual machine. The command that I am running after I set up the environment and convert the file structure is recon-all -s TED -all. Then I tried recon-all -s TED -autorecon1
I have tried this on a couple of different subjects and have tried deleting and cleaning up the directories and remaking them, checking to make sure that I have enough hard drive space etc., but I keep getting the same error messages.
Below are the error messages that I am receiving.
Thanks for you time.
Sincerely, Max
Max Gunther, PhD
Vanderbilt University Medical Center Departments of Psychiatry and Medicine Center for Health Services Research Nashville, TN www.ICUdelirium.org
freesurfer@freesurfer-virtual:/mnt$ ls 2190 Ely_2190_3_1-0001.nii Ely_2405_3_1 Ely_786_3_1 AJM Ely_2206_3_1 Ely_2409_3_1 HMN CBB Ely_2231_3_1 Ely_2448_3_1 TED Ely_1204_3_1 Ely_2290_3_1 Ely_2461_3_1 TED.nii Ely_2178_3_1 Ely_2373_3_1 Ely_783_3_1 Ely_2190_3_1 Ely_2376_3_1 Ely_783_3_1-0001.nii freesurfer@freesurfer-virtual:/mnt$ freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED.nii -force ERROR: nothing to do freesurfer@freesurfer-virtual:/mnt$ freesurfer@freesurfer-virtual:/mnt$ freesurfer@freesurfer-virtual:/mnt$ freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -i TED.nii -force INFO: /mnt/TED exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt Actual FREESURFER_HOME /usr/local/freesurfer Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /mnt/TED
mri_convert /mnt/TED.nii /mnt/TED/mri/orig/001.mgz
mri_convert /mnt/TED.nii /mnt/TED/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /mnt/TED.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997863, 0.0653316, -0.000653581) j_ras = (0.0653335, 0.997724, -0.01666) k_ras = (0.000436332, 0.0166671, 0.999861) writing to /mnt/TED/mri/orig/001.mgz...
#------------------------------------------
recon-all finished without error at Thu Jul 22 21:34:41 EDT 2010 done freesurfer@freesurfer-virtual:/mnt$ recon-all -s 2190 -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwxrwx 1 root root 31066267445 Jul 22 21:25 /mnt/2190/scripts/recon-all.log Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux tee: /mnt/2190/scripts/recon-all.log: Protocol error #-------------------------------------------- tee: /mnt/2190/scripts/recon-all.log: Protocol error #@# MotionCor Thu Jul 22 21:36:51 EDT 2010 tee: /mnt/2190/scripts/recon-all.log: Protocol error Found 1 runs tee: /mnt/2190/scripts/recon-all.log: Protocol error /mnt/2190/mri/orig/001.mgz tee: /mnt/2190/scripts/recon-all.log: Protocol error WARNING: only one run found. This is OK, but motion tee: /mnt/2190/scripts/recon-all.log: Protocol error correction cannot be performed on one run, so I'll tee: /mnt/2190/scripts/recon-all.log: Protocol error copy the run to rawavg and continue. tee: /mnt/2190/scripts/recon-all.log: Protocol error
cp /mnt/2190/mri/orig/001.mgz /mnt/2190/mri/rawavg.mgz
tee: /mnt/2190/scripts/recon-all.log: Protocol error ^C freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwxrwx 1 root root 1883387 Jul 22 21:34 /mnt/TED/scripts/recon-all.log Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux #-------------------------------------------- #@# MotionCor Thu Jul 22 21:37:17 EDT 2010 Found 1 runs /mnt/TED/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /mnt/TED/mri/orig/001.mgz /mnt/TED/mri/rawavg.mgz
/mnt/TED
mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform
mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /mnt/TED/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997863, 0.0653316, -0.000653581) j_ras = (0.0653335, 0.997724, -0.01666) k_ras = (0.000436332, 0.0166671, 0.999861) Original Data has (0.9375, 0.9375, 4.93393) mm size and (256, 256, 28) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 3 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/TED/mri/orig.mgz...
mri_add_xform_to_header -c /mnt/TED/mri/transforms/talairach.xfm /mnt/TED/mri/orig.mgz /mnt/TED/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- tee: /mnt/TED/scripts/recon-all.log: Protocol error #@# Nu Intensity Correction Thu Jul 22 22:01:19 EDT 2010 tee: /mnt/TED/scripts/recon-all.log: Protocol error
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
tee: /mnt/TED/scripts/recon-all.log: Protocol error /mnt/TED/mri tee: /mnt/TED/scripts/recon-all.log: Protocol error /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7.2.2 2009/05/04 16:16:27 nicks Exp $ Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux Thu Jul 22 22:01:20 EDT 2010 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2007-11-01 at 16:24:51 tmpdir is ./tmp.mri_nu_correct.mni.26799 /mnt/TED/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26799/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26799/nu0.mnc ncendef: ncid 3: Protocol error Error outputting volume: possibly disk full? $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.7153e-09, -8.45737e-11) j_ras = (-3.36186e-10, -3.63052e-09, -1) k_ras = (-1.90607e-08, 1, 2.12146e-09) writing to ./tmp.mri_nu_correct.mni.26799/nu0.mnc... ERROR: mincWrite: output_volume exited with 1 ERROR: failure writing ./tmp.mri_nu_correct.mni.26799/nu0.mnc ERROR: converting to minc tee: /mnt/TED/scripts/recon-all.log: Protocol error Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
tee: /mnt/TED/scripts/recon-all.log: Protocol error recon-all exited with ERRORS at Thu Jul 22 22:01:27 EDT 2010 tee: /mnt/TED/scripts/recon-all.log: Protocol error
tee: /mnt/TED/scripts/recon-all.log: Protocol error freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -autorecon1 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwxrwx 1 root root 30978108369 Jul 22 22:01 /mnt/TED/scripts/recon-all.log Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux tee: /mnt/TED/scripts/recon-all.log: Protocol error #-------------------------------------------- tee: /mnt/TED/scripts/recon-all.log: Protocol error #@# MotionCor Fri Jul 23 13:02:59 EDT 2010 tee: /mnt/TED/scripts/recon-all.log: Protocol error Found 1 runs tee: /mnt/TED/scripts/recon-all.log: Protocol error /mnt/TED/mri/orig/001.mgz tee: /mnt/TED/scripts/recon-all.log: Protocol error WARNING: only one run found. This is OK, but motion tee: /mnt/TED/scripts/recon-all.log: Protocol error correction cannot be performed on one run, so I'll tee: /mnt/TED/scripts/recon-all.log: Protocol error copy the run to rawavg and continue. tee: /mnt/TED/scripts/recon-all.log: Protocol error
cp /mnt/TED/mri/orig/001.mgz /mnt/TED/mri/rawavg.mgz
tee: /mnt/TED/scripts/recon-all.log: Protocol error /mnt/TED tee: /mnt/TED/scripts/recon-all.log: Protocol error
mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform
tee: /mnt/TED/scripts/recon-all.log: Protocol error mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform tee: /mnt/TED/scripts/recon-all.log: Protocol error $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /mnt/TED/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997863, 0.0653316, -0.000653581) j_ras = (0.0653335, 0.997724, -0.01666) k_ras = (0.000436332, 0.0166671, 0.999861) Original Data has (0.9375, 0.9375, 4.93393) mm size and (256, 256, 28) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 3 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/TED/mri/orig.mgz... tee: /mnt/TED/scripts/recon-all.log: Protocol error Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
tee: /mnt/TED/scripts/recon-all.log: Protocol error recon-all exited with ERRORS at Fri Jul 23 13:03:10 EDT 2010 tee: /mnt/TED/scripts/recon-all.log: Protocol error
tee: /mnt/TED/scripts/recon-all.log: Protocol error freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -autorecon1