Dear FreeSurfers,<div><br></div><div>I am new to FreeSurfer and just trying to run some simple volumetric analysis and I get a &quot;Protocol error&quot;.</div><div><br></div><div>I went to look at the log file and it is 30 gigabytes in size so something is going awry here...</div>
<div><br></div><div>Is there a way to break this error down further to understand what may be going wrong?</div><div><br></div><div>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</div>
<div><br></div><div>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.</div>
<div><br></div><div>Below are the error messages that I am receiving.</div><div><br></div><div>Thanks for you time.</div><div><br></div><div>Sincerely,</div><div>Max<br clear="all"><br>Max Gunther, PhD<br><br>Vanderbilt University Medical Center<br>
Departments of Psychiatry and Medicine<br>Center for Health Services Research<br>Nashville, TN <a href="http://www.ICUdelirium.org">www.ICUdelirium.org</a><br><br></div><div><br></div><div><div>freesurfer@freesurfer-virtual:/mnt$ ls</div>
<div>2190          Ely_2190_3_1-0001.nii  Ely_2405_3_1          Ely_786_3_1</div><div>AJM           Ely_2206_3_1           Ely_2409_3_1          HMN</div><div>CBB           Ely_2231_3_1           Ely_2448_3_1          TED</div>
<div>Ely_1204_3_1  Ely_2290_3_1           Ely_2461_3_1          TED.nii</div><div>Ely_2178_3_1  Ely_2373_3_1           Ely_783_3_1</div><div>Ely_2190_3_1  Ely_2376_3_1           Ely_783_3_1-0001.nii</div><div>freesurfer@freesurfer-virtual:/mnt$ </div>
<div>freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED.nii -force</div><div>ERROR: nothing to do</div><div>freesurfer@freesurfer-virtual:/mnt$ </div><div>freesurfer@freesurfer-virtual:/mnt$ </div><div>freesurfer@freesurfer-virtual:/mnt$ </div>
<div>freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -i TED.nii -force</div><div>INFO: /mnt/TED exists with -i, but -force specified.</div><div>Deleting any previous source volumes</div><div>Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0</div>
<div>Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0</div><div>INFO: SUBJECTS_DIR is /mnt</div><div>Actual FREESURFER_HOME /usr/local/freesurfer</div><div>Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux</div>
<div>/mnt/TED</div><div><br></div><div> mri_convert /mnt/TED.nii /mnt/TED/mri/orig/001.mgz </div><div><br></div><div>mri_convert /mnt/TED.nii /mnt/TED/mri/orig/001.mgz </div><div>$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $</div>
<div>reading from /mnt/TED.nii...</div><div>TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00</div><div>i_ras = (-0.997863, 0.0653316, -0.000653581)</div><div>j_ras = (0.0653335, 0.997724, -0.01666)</div><div>k_ras = (0.000436332, 0.0166671, 0.999861)</div>
<div>writing to /mnt/TED/mri/orig/001.mgz...</div><div><br></div><div>#------------------------------------------</div><div><br></div><div>recon-all finished without error at Thu Jul 22 21:34:41 EDT 2010</div><div>done</div>
<div>freesurfer@freesurfer-virtual:/mnt$ recon-all -s 2190 -all</div><div>Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0</div><div>Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0</div><div>INFO: SUBJECTS_DIR is /mnt</div>
<div>Actual FREESURFER_HOME /usr/local/freesurfer</div><div>-rwxrwxrwx 1 root root 31066267445 Jul 22 21:25 /mnt/2190/scripts/recon-all.log</div><div>Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux</div>
<div>tee: /mnt/2190/scripts/recon-all.log: Protocol error</div><div>#--------------------------------------------</div><div>tee: /mnt/2190/scripts/recon-all.log: Protocol error</div><div>#@# MotionCor Thu Jul 22 21:36:51 EDT 2010</div>
<div>tee: /mnt/2190/scripts/recon-all.log: Protocol error</div><div>Found 1 runs</div><div>tee: /mnt/2190/scripts/recon-all.log: Protocol error</div><div>/mnt/2190/mri/orig/001.mgz</div><div>tee: /mnt/2190/scripts/recon-all.log: Protocol error</div>
<div>WARNING: only one run found. This is OK, but motion</div><div>tee: /mnt/2190/scripts/recon-all.log: Protocol error</div><div>correction cannot be performed on one run, so I&#39;ll</div><div>tee: /mnt/2190/scripts/recon-all.log: Protocol error</div>
<div>copy the run to rawavg and continue.</div><div>tee: /mnt/2190/scripts/recon-all.log: Protocol error</div><div><br></div><div> cp /mnt/2190/mri/orig/001.mgz /mnt/2190/mri/rawavg.mgz </div><div><br></div><div>tee: /mnt/2190/scripts/recon-all.log: Protocol error</div>
<div>^C</div><div>freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -all</div><div>Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0</div><div>Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0</div><div>
INFO: SUBJECTS_DIR is /mnt</div><div>Actual FREESURFER_HOME /usr/local/freesurfer</div><div>-rwxrwxrwx 1 root root 1883387 Jul 22 21:34 /mnt/TED/scripts/recon-all.log</div><div>Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux</div>
<div>#--------------------------------------------</div><div>#@# MotionCor Thu Jul 22 21:37:17 EDT 2010</div><div>Found 1 runs</div><div>/mnt/TED/mri/orig/001.mgz</div><div>WARNING: only one run found. This is OK, but motion</div>
<div>correction cannot be performed on one run, so I&#39;ll</div><div>copy the run to rawavg and continue.</div><div><br></div><div> cp /mnt/TED/mri/orig/001.mgz /mnt/TED/mri/rawavg.mgz </div><div><br></div><div>/mnt/TED</div>
<div><br></div><div> mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform </div><div><br></div><div>mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform </div><div>$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $</div>
<div>reading from /mnt/TED/mri/rawavg.mgz...</div><div>TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00</div><div>i_ras = (-0.997863, 0.0653316, -0.000653581)</div><div>j_ras = (0.0653335, 0.997724, -0.01666)</div><div>k_ras = (0.000436332, 0.0166671, 0.999861)</div>
<div>Original Data has (0.9375, 0.9375, 4.93393) mm size and (256, 256, 28) voxels.</div><div>Data is conformed to 1 mm size and 256 voxels for all directions</div><div>changing data type from 3 to 0 (noscale = 0)...</div>
<div>MRIchangeType: Building histogram </div><div>Reslicing using trilinear interpolation </div><div>writing to /mnt/TED/mri/orig.mgz...</div><div><br></div><div> mri_add_xform_to_header -c /mnt/TED/mri/transforms/talairach.xfm /mnt/TED/mri/orig.mgz /mnt/TED/mri/orig.mgz </div>
<div><br></div><div>INFO: extension is mgz</div><div>#--------------------------------------------</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>#@# Nu Intensity Correction Thu Jul 22 22:01:19 EDT 2010</div>
<div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div><br></div><div> mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 </div><div><br></div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>/mnt/TED/mri</div>
<div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>/usr/local/freesurfer/bin/mri_nu_correct.mni</div><div>--i orig.mgz --o nu.mgz --n 2</div><div>nIters 2</div><div>$Id: mri_nu_correct.mni,v 1.7.2.2 2009/05/04 16:16:27 nicks Exp $</div>
<div>Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux</div><div>Thu Jul 22 22:01:20 EDT 2010</div><div>Program nu_correct, built from:</div><div>Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2007-11-01 at 16:24:51</div>
<div>tmpdir is ./tmp.mri_nu_correct.mni.26799</div><div>/mnt/TED/mri</div><div>mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26799/nu0.mnc</div><div>mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26799/nu0.mnc </div><div>ncendef: ncid 3: Protocol error</div>
<div>Error outputting volume: possibly disk full?</div><div>$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $</div><div>reading from orig.mgz...</div><div>TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00</div><div>
i_ras = (-1, 4.7153e-09, -8.45737e-11)</div><div>j_ras = (-3.36186e-10, -3.63052e-09, -1)</div><div>k_ras = (-1.90607e-08, 1, 2.12146e-09)</div><div>writing to ./tmp.mri_nu_correct.mni.26799/nu0.mnc...</div><div>ERROR: mincWrite: output_volume exited with 1</div>
<div>ERROR: failure writing ./tmp.mri_nu_correct.mni.26799/nu0.mnc</div><div>ERROR: converting to minc</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux</div>
<div><br></div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>recon-all exited with ERRORS at Thu Jul 22 22:01:27 EDT 2010</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div><br></div>
<div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -autorecon1</div><div>Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0</div><div>Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0</div>
<div>INFO: SUBJECTS_DIR is /mnt</div><div>Actual FREESURFER_HOME /usr/local/freesurfer</div><div>-rwxrwxrwx 1 root root 30978108369 Jul 22 22:01 /mnt/TED/scripts/recon-all.log</div><div>Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux</div>
<div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>#--------------------------------------------</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>#@# MotionCor Fri Jul 23 13:02:59 EDT 2010</div>
<div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>Found 1 runs</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>/mnt/TED/mri/orig/001.mgz</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div>
<div>WARNING: only one run found. This is OK, but motion</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>correction cannot be performed on one run, so I&#39;ll</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div>
<div>copy the run to rawavg and continue.</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div><br></div><div> cp /mnt/TED/mri/orig/001.mgz /mnt/TED/mri/rawavg.mgz </div><div><br></div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div>
<div>/mnt/TED</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div><br></div><div> mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform </div><div><br></div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div>
<div>mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform </div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $</div><div>reading from /mnt/TED/mri/rawavg.mgz...</div>
<div>TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00</div><div>i_ras = (-0.997863, 0.0653316, -0.000653581)</div><div>j_ras = (0.0653335, 0.997724, -0.01666)</div><div>k_ras = (0.000436332, 0.0166671, 0.999861)</div><div>Original Data has (0.9375, 0.9375, 4.93393) mm size and (256, 256, 28) voxels.</div>
<div>Data is conformed to 1 mm size and 256 voxels for all directions</div><div>changing data type from 3 to 0 (noscale = 0)...</div><div>MRIchangeType: Building histogram </div><div>Reslicing using trilinear interpolation </div>
<div>writing to /mnt/TED/mri/orig.mgz...</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux</div><div>
<br></div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>recon-all exited with ERRORS at Fri Jul 23 13:03:10 EDT 2010</div><div>tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div><br></div><div>
tee: /mnt/TED/scripts/recon-all.log: Protocol error</div><div>freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -autorecon1</div><div><br></div><br></div>