Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

prefrontal gyrification
by melinda dora 03 Sep '14

03 Sep '14

Dear list, how would I get gyrification for the prefrotnal cortex? there is no annotation for this structure? Do I need to make my own? and if so, how? best, Melly

2 1

mkanalysis-sess blocked design
by Milde, Christopher 03 Sep '14

03 Sep '14

Dear Freesurfer Experts, I want to run mkanalysis-sess for a blocked design, but unfortunately only the flags -abblocked, -event-related, -retinotopy and -notask do exist. How can I specify the designtype for a blocked design with one condition and on fixation with different block lengths for condition and fixation? I'm using Freesurfer 5.3 Thanks in advance, Chris

1 1

Group cortical thickness QDEC help
by Taylor North 02 Sep '14

02 Sep '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 0

Job offer: 1 PhD and 1 PostDoc in Neuroimaging of Epilepsy - Tübingen, Germany
by Niels Focke 02 Sep '14

02 Sep '14

We currently have two open job opportunities at the University of Tübingen, Germany. Both in the field of neuroimaging in epilepsy. 1) PostDoc to work on post-processing of functional and structural MRI / network analysis (graph-theory, classification algorithms, EEG-fMRI) 2) PhD-Student to work on structural post-processing using multispectral MRI and automated lesion detection Details can be found on: http://www.hih-tuebingen.de/stellenangebote/stellenangebote-fuer-wissenschaf tler/translational-neuroimaging-ag-focke Short-URL: http://goo.gl/bA5h1D __________________________________________________________________________ Dr. Niels Focke Oberarzt Abt. Neurologie mit Schwerpunkt Epileptologie Universitätsklinikum Tübingen AG Translationale Bildgebung Hertie Institut für Klinische Hirnforschung Werner Reichhardt Centre for Integrative Neuroscience

1 0

longitudinal base problem - bad surfaces
by Koolschijn, Cédric 02 Sep '14

02 Sep '14

Dear experts, I'm performing a longitudinal analysis, and have done so before, but I encounter an error after running -base for one subject which I haven't seen before. The cross surfaces of both timepoints look OK, but the base surface is seems to be shrunken for unknown reasons. I reran all steps, but with the same results. The log file also doesn't provide any useful information, no errors were reported. Below, please find screenshots of the surfaces for each tp. tp1: https://www.dropbox.com/s/5cwksrzqyw9jxxo/n4t1.tif?dl=0 tp2: https://www.dropbox.com/s/858062gh1uwigo2/n4t2.tif?dl=0 base: https://www.dropbox.com/s/hutaarl7jvthwcy/n4base.tif?dl=0 Do you have any idea what caused the mess-up in -base, and how to fix this? It will be a lot of editing should this be done manually, so I'm hoping for a better option. Many thanks! Best, Cédric

2 1

Questions about mri_make_bem_surfaces function
by gamaliel huerta urrea 01 Sep '14

01 Sep '14

Hi experts I need use the mri_make_bem_surfaces function to generate the three surfaces from brain MRIs patient exam. I have installed Freesurfer and I have my series of MRIs in 001.mgz file. would be helpful if you could provide some material to use this function. regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso*

1 0

questions about qdec, group and age interaction
by yaya ya 01 Sep '14

01 Sep '14

Dear all, I encountered several questions when using freesurfer. Although I searched carefully in this mailing list, I am still not very clear about some issues. My issues are described below: Based on a bunch of information, I know that before describing my results, I need to check whether there is an interaction effects between group and age. In order to do it, I demean my age variable and add it as a continuous covariate in Qdec. My discrete variable is group. Then I run the analysis on cortical thickness, producing several results. But I am not very sure about which of them described the group*age interaction effects in my data so that I could check the interaction results. That is why I need your help with confirming it. The name of several results are listed here: 1. does the average thickness differ from zero? (I don't think this is interacton effect) 2. does the correlation between thickness and demean-age, accounting for group, differ from zero? (this is not the interaction either. this should be the relation between thickness and age across 2 groups.) 3. does the average thickness differe between the two groups? (this should be the group main effect) 4, does the thickness-age correlation differ between 2 groups (*I think this should be what I need*). If so, I further checked whether the fourth one could survive the corrected threshold using monte carlo stimulation (threshold 1.3, p<0.05). two clusters survived. But one interesting thing is that the results from above 3 and 4 produced the same results except one thing. 3 gave the hightened thickness of several regions in patients groups compared with controls. In contrast, 4 found the same region but the opposite pattern (decresed thickness in patients compared with controls). When I add my age as a nuisance covariate, I get the same results 3. I don't know which one should report. Do my results make sense? My last question is that I could not find the data file which includes the thickness values from each subject resulting from above analysis because I want to do some correlation analysis with other clinical variables. I hope that it is clear to you all. Thank you for your help in advance. Best, Lickey

1 0

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

1 1

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