Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Change in the location/path and the name of subject
by Reza Rajimehr 01 Sep '14

01 Sep '14

Hi, I have got anatomicals of a subject from someone else. The anatomicals have been processed, and the surfaces have been reconstructed. The path to these files in my machine is obviously different from the path where data have been analyzed. I also want to change the name of the subject and give a name based on a convention that I have for my other subjects. Would the change in the location and name of the subject be problematic later on when I want to work with the anatomical data or use them during the functional data analysis? (re-processing of the anatomicals is not an option, since these are monkey data with heavy amounts of manual editings) Thanks, Reza

3 2

license file problem solved
by Philipp G. Sämann 30 Aug '14

30 Aug '14

Hi all, the license file problem I have described earlier today could be solved by following earlier hints on a workaround, mainly in the following two contributions: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29404.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29433.html It turned out to be the same problem: by an update of the SuSe system (from an old system 11.x to 13.x), the libcrypt.so.1 tool could not be used any more. Copying an old version (of an old SuSe system) to the freesurfer/lib folder, linking it and adding the folder to the LD_LIBRARY_PATH worked out... I think the problem should be pointed out in the installation instructions. The error message (I am not a sys admin...) that the license file is not valid was very misleading. Best wishes, Philipp I am stuck with a license error in that freesurfer (after a simple recon-all call for segmentation) continues to interrupt the process soon after starting it, see complete copy of the error log file below. I have freshly installed Freesurfer FROM SCRATCH and applied for a new licence file which lies at the appropriate location. What does "INVALID LICENSE FILE" actually indicate, how can the file be invalid? What can be done and why does the programm run absolutely smoothly on another Linux-64-bit system?? vG Philipp Sat Aug 30 17:17:48 CEST 2014 /net/PE1/raid1/enigma-mdd/data/WG_989 /net/PE1/raid1/enigma-mdd/freesurfer/bin/recon-all -subjid WG_989 -all -hippo-subfields subjid WG_989 setenv SUBJECTS_DIR /net/PE1/raid1/enigma-mdd/data FREESURFER_HOME /net/PE1/raid1/enigma-mdd/freesurfer Actual FREESURFER_HOME /net/PE1/raid1/enigma-mdd/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux PE3 3.11.6-4-desktop #1 SMP PREEMPT Wed Oct 30 18:04:56 UTC 2013 (e6d4a27) 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 2066987 maxlocks unlimited maxsignal 2066987 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 264665936 263134184 1531752 0 194912 255250340 -/+ buffers/cache: 7688932 256977004 Swap: 20972820 4929156 16043664 ######################################## 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 $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /net/PE1/raid1/enigma-mdd/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /net/PE1/raid1/enigma-mdd/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Sat Aug 30 17:17:53 CEST 2014 Found 1 runs /net/PE1/raid1/enigma-mdd/data/WG_989/mri//001.mgz Checking for (invalid) multi-frame inputs... 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 /net/PE1/raid1/enigma-mdd/data/WG_989/mri//001.mgz /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz /net/PE1/raid1/enigma-mdd/data/WG_989 mri_convert /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz /net/PE1/raid1/enigma-mdd/data/WG_989/mri/orig.mgz --conform mri_convert /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz /net/PE1/raid1/enigma-mdd/data/WG_989/mri/orig.mgz --conform -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /net/PE1/raid1/enigma-mdd/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz... Linux PE3 3.11.6-4-desktop #1 SMP PREEMPT Wed Oct 30 18:04:56 UTC 2013 (e6d4a27) x86_64 x86_64 x86_64 GNU/Linux recon-all -s WG_989 exited with ERRORS at Sat Aug 30 17:17:57 CEST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Max-Planck-Institut für Psychiatrie AG Kernspintomographie Kraepelinstr. 2-10 80804 München Tel. 089-30622-413 Fax 089-30622-520

1 0

Group cortical thickness QDEC help
by Taylor North 30 Aug '14

30 Aug '14

Hello, I am having some troubles using QDEC to analyze the thickness changes in my group study and I was hoping someone may be able to give me a hand. The steps I have done are as follows: I am working on a study looking at 40 subjects scanned at two time points (base and 6 months after). I have followed all the steps for longitudinal processing for each subject (cross,base, and longitudinals) and made edits where they were necessary to the base. I then entered all 40 subjects into a QDEC table as follows fsid fsid-base time gender age crosstpN1 base1 0 female 20 crosstpN2 base1 6 female 20 .......... continues for rest of the subjects then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and then transformed the longitudinal QDEC table into a QDEC table which looks like: fsid time gender age Base1 3 female 20 .......... continues for the rest of the subjects. I then followed the QDEC steps outlined In the group tutorial. (import cross sectional table, generate stats data table, import aseg volume, set longitudinal dependent variables and pick continuous variable. 1) the first problem I am having is that when I go to process the longitudinal group results through QDEC it makes me pick a continuous variable when I just want to analyze the dependent variable The symmetrized percent change. So I have tried picking different continuous variables ( such as age or importing rhcortex volume etc...) with choosing symmetrized percent change as the dependent variable. No matter what continuous variable I pick the question: ``does the average symmetrized percent change differ from zero"? always comes up, the problem is depending on what continuous variable I pick the results change. Is there a way to just look at the longitudinal thickness changes across a group alone, because I first want to look at the atrophy across the whole group over 6 months and then compare the differences in atrophy against the diagnosed and non diagnosed group. 2) another thing I don't quite understand is it seems like the longitudinal qdec tables are made with the cross of the subjects under fsid, but why wouldn't you use the longitudinals under the fsid for the longitudinal table instead? Also it seems like in the cross sectional qdec table the base is the subject being analyzed under fsid, which also doesn't make sense to me because in the tutorial it says base should not be used directly for analysis. thanks for the help! Taylor

1 1

mri_watershed: really bad skull stripping
by Úrsula Pérez Ramírez 30 Aug '14

30 Aug '14

Hello, I’m new with FreeSurfer and I’m getting a really bad skull stripping (almost nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerably. I have tried with a subject from the tutorial dataset and it’s OK. What can be the problem? Thank you very much! Úrsula

3 6

cortical thickness analysis
by Xinfa Shi 30 Aug '14

30 Aug '14

Hi , I want to make a cortical thickness analysis ,and could you provide me for a user guide or tool ? Regards. Xin-Fa Shi.

2 1

Longitudinal troubleshooting
by Janosch Linkersdörfer 29 Aug '14

29 Aug '14

Hi Martin and all, I am about to process a large longitudinal dataset (normal development, no patients) and wanted to ask about the best (i.e., time efficient) strategy for troubleshooting. If I understand correctly from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits, it might be OK in my case (only little longitudinal changes expected) to only edit the base runs and transfer those edits to the long runs. So I thought of doing the following: - use the QA tools to export detailed snapshots of all base runs - check the snapshots for errors - use Freeview to add control points / edit white matter in brainmask.mgz of the base runs (while simultaneously checking whether those edits would make sense in brainmask.mgz of all long runs of the same subject) - rerun base - rerun longs Does that make sense? Thanks, Janosch

2 1

Reconstruct tm3d warp from mri_cvs_register
by Makaretz, Sara Johanna 29 Aug '14

29 Aug '14

Hi all, I ran mri_cvs_register but forgot to add --nocleanup. I have the final combined m3z and no tm3d, and for el_reg just mgz files. Can I recreate the tm3d combined with just these files? On the wiki it says use createMorph - I tried different inputs in 5.3 and dev environments with no success. (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register) Thanks, Sara

1 0

Re: [Freesurfer] recon-all normalization: bias field output
by Barbara Kreilkamp 29 Aug '14

29 Aug '14

Dear Freesurfers, The recon-all.log does not give info about the intermediate outputs (like nu2_est and nu2_field mnc-files), could you please confirm that the nu2_field.mnc is the bias field volume? It is the biggest file of all and is one of the last files generated by the script, but I would like to be sure. Thank you very much, Barbara On Thu, Aug 28, 2014 at 3:27 PM, Barbara Kreilkamp <bakk.hbg(a)googlemail.com> wrote: > Dear Bruce and Christian, > > I found the easy way of simply writing 'set cleanup = 0' at the beginning > of mri_nu_correct.mni and then I run this command > mri_nu_correct.mni --i T2-scic/mri/orig/001.mgz --o nu.mgz --n 2 > > This way I get all the masks and iterations that were computed. > > Now I also see that it generates as many folders as there are iterations, > ending with nu2_field and nu2_est if there are two iterations. I see more > files now and now I am thinking that the last output is nu2_field, which > would be the bias field. > So this is why I did not divide anything by hand (also because my 001.mgz > and the nu.mgz do not have the same image dimensions) and the info about > masked-out voxel would be missing in that case. > > All the best and thanks. > Barbara > > > > On 28/08/2014 14:46, Bruce Fischl wrote: > >> Hi Barbara >> what exactly did you divide? If you look at the recon-all.log it will >> show the exact inputs and outputs of nu_correct. >> >> cheers >> Bruce >> >> >> On Thu, 28 Aug 2014, Barbara Kreilkamp wrote: >> >> Dear Christian, >>> >>> Thanks a bunch for this answer. I ran all the steps you mentioned >>> (except for the one where I simply do uncorrected/corrected, as these >>> images have different dimensions, it seems nu3 does more than just >>> normalization of intensities, but also image cropping). Do you know >>> anything about the image cropping? >>> >>> I ended up with the output nu1_mask and nu1_est and I think the last one >>> is the bias field, at least it looks very much like one :). Am I right? >>> >>> Thanks for your help, >>> Barbara >>> >>> >>> On 27/08/2014 22:53, Christian Thode Larsen wrote: >>> >>>> Hi Barbara, >>>> >>>> I'm not aware of any way that you can do it directly by passing >>>> arguments to recon-all (some might correct me on that), but it is >>>> possible: >>>> >>>> 1) As N3 models the bias as a multiplicative effect uncorrected = >>>> corrected * bias, the simplest way is to divide each voxel of the volume >>>> before and after correction, in order to obtain a volume containing the >>>> bias. Note that N3 (by default) works within a mask where low-intensity >>>> voxels have been thresholded away. These voxels will contain garbage if >>>> you divide all voxels in the volume. >>>> >>>> 2) Somewhat more complicated: you can specify the -keeptmp flag combined >>>> with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to >>>> preserve its working files. This requires you to modify the N3 binary >>>> call in the mri_nu_correct.mni script. You also need to convert the mnc >>>> files from the tmp dir, so that you can work with the volumes. >>>> >>>> 3) if you do 2), you also get hold of the low-intensity voxel mask that >>>> N3 operates within. You can use this to constrain the division mentioned >>>> in 1). >>>> >>>> Best, >>>> Christian >>>> >>>> On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote: >>>> >>>>> Dear all, >>>>> >>>>> Is there a way to output the N3's (non-parametric normalization step) >>>>> output? >>>>> I am interested in the bias field that was computed to correct the >>>>> image >>>>> intensities. >>>>> >>>>> Thank you for your help, >>>>> Barbara >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)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(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >

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Post-doctoral opportunity (and beyond) in neuroimaging analysis
by Willem Huijbers 29 Aug '14

29 Aug '14

PostDoc (or beyond) in Neuro Image Analysis: Magnetic Resonance Imaging – Code 1267/2014/8 Description: Population Health Sciences at the DZNE aims to investigate causes and preclinical biomarkers of neurodegenerative diseases, and to study normal and pathological brain structure and function over the adult life course. To this end we are currently establishing the Rhineland Study, a prospective population based cohort study that will include up to 30,000 people aged 30 years and over. The study facilities will encompass 3 dedicated examination centers equipped with state-of-the art 3T MRI scanners (Siemens Prisma), advanced bio-banking facilities and large data storage and computational clusters for analysis of big data.All study participants will undergo extensive phenotyping. This encompasses repeated and detailed brain imaging, including structural (T1, T2, T2*) and functional imaging (DTI, perfusion and BOLD imaging). A subset of the cohort will additionally be followed with 7T imaging and possibly PET imaging. We are looking for enthusiastic and ambitious researchers who will contribute to the further development of neuro image analysis in the framework of the Rhineland Study. The qualified applicant should have a PhD in neuro-image analysis, cognitive neuroscience, computer science or related field and a strong research background in large-scale neuroimage processing or population neuroimaging. Applicants should have experience with existing tools for large-scale analysis of neuroimaging data (e.g. with SPM, FSL, AFNI, etc.), relevant programming experience (e.g. with MATLAB, Python), and proficiency in mathematics and statistics (R, SPSS). Working experience in epidemiological research or large-scale clinical studies is highly desirable. Demonstrable interest in quantitative research, strong analytical skills, ability for independent and critical thinking, and excellent communication and writing skills in the English language are a prerequisite. Creative, highly motivated and team-oriented candidates who dare to take initiative and enjoy working in a fast-growing, dynamic research environment in an internationally oriented biomedical institution, are strongly encouraged to apply. We offer a scientific position with a long-term perspective. The position is initially limited to two years with the possibility of extension. For further information, please contact Prof Monique M.B. Breteler (rhinelandstudy(a)dzne.de) Also, feel free to contact me if you are interested or if you want more information Willem Huijbers

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Using FS v5.3 for group analysis with recon-all done with FS v5.0
by Matthieu Vanhoutte 29 Aug '14

29 Aug '14

Dear experts, I'd like to use Freesurfer v5.3 to make group analysis on quantitative CBF maps computed in volume and projected on fsaverage surface. Knowing that all my subjects have been recon-all with FS v5.0, is this neccesary to me to relaunch recona-all to all my subjects with FS v5.3 before I do my group analysis ? Precisely, until now I have only used from FS v5.0 : -> "T1.mgz" to register ASL on anatomical -> "mri_vol2surf" to project CBF maps on fsaverage surface and smooth them Thank you for replying ! Best, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France

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