Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS
by falk.luesebrink＠med.ovgu.de 25 Jan '19

25 Jan '19

External Email - Use Caution I was able to circumvent the error by switching from python3 to python2. In python3 print was changed to a function making it necessary to put the arguments in brackets. Best, Falk Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Im Auftrag von falk.luesebrink(a)med.ovgu.de Gesendet: Freitag, 25. Januar 2019 10:42 An: Freesurfer Mailinglist <freesurfer(a)nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS External Email - Use Caution Dear Juergen, Thanks for your quick reply! Actually the spelling error is in the error message. Taken from http://martinos.org/~mreuter/long/long_mris_slopes # extensive error checks # if options.fsgd is None and if options.qdec is None: # print 'ERROR: Specify --fsgd or --qedc' parser.print_help() print '\nERROR: Specify --qedc (and other required arguments)\n' sys.exit(1) # if options.fsgd is not None and options.qdec is not None: # print 'ERROR: Specify either --fsgd or --qedc, not both' # sys.exit(1) At least Martin is consistent with his typo. :D Best, Falk Von: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> Im Auftrag von Juergen Haenggi Gesendet: Freitag, 25. Januar 2019 10:35 An: Freesurfer Mailinglist <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS External Email - Use Caution Dear Falk I have no idea, but recognised that the error refers to --qedc and not to --qdec. maybe there is a spelling error somewhere that is related to your problem. HTH Cheers Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch<mailto:j.haenggi@psychologie.uzh.ch> (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. ----------------------------------------------------------------------------------------------------- On 25 Jan 2019, at 10:26, falk.luesebrink(a)med.ovgu.de<mailto:falk.luesebrink@med.ovgu.de> wrote: External Email - Use Caution Dear all, Has anyone run the longitudinal pipeline successfully using the WSL? I’m running it with Ubuntu 18.04.1 LTS and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I’m trying to process my first longitudinal data set following the instructions of the tutorial as close as possible. The data has been processed without issues and now I want to do the statistical analysis. When I run: long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR I get the following error: File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448 print '\nERROR: Specify --qedc (and other required arguments)\n' ^ SyntaxError: invalid syntax I get comparable errors for any other long_* command I try to run, e.g. long_qdec_table with or without any arguments gives: File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119 print '\nERROR: Specify --qedc' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('\nERROR: Specify --qedc')? Does anyone have a clue where this error originates from using either WSL or Ubuntu 18.04? Best, Falk ............................................... <image001.gif> Universitätsklinik für Neurologie Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg Telefon: +49-391-6117-512 falk.luesebrink(a)med.ovgu.de<mailto:falk.luesebrink@med.ovgu.de> http://www.kneu.ovgu.de/kneu.html _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

correction for multiple comparison: simulation vs grf vs cache
by john Anderson 24 Jan '19

24 Jan '19

External Email - Use Caution Hi Dr Greve, I would like to correct surface based analyses of PET data for multiple comparisons. I ran group comparisons in three spaces. left and right hemispheres and subcortical. I used the method --cache in mri_glmfit-sim to correct the analyses in eft and right hemispheres. I used the method --grf in mri_glmfit-sim to correct the analyses in subcortical regions. My questions are: In one of your kind responses to a collegue here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-January/035650.… you had suggested "If you want to use GRF, you should use smooth by twice the native voxel size. I would not go higher than .01 on the threshold". Would you mind clarify what it means don;t go higher than .01 is this the cwp threshold? also smoothing by twice the native voxel is this means fwhm=2mm? The methods --cache and --grf are giving me the expected results.. when I should consider using simulation --perm ? Thanks for any clarification John

2 1

Smoothing before or after PALM (and results conversion for Surf Ice)
by Daniel Leopold 24 Jan '19

24 Jan '19

External Email - Use Caution Hello FS experts and enthusiasts, Thus far, I have used mri_concat to make 4D files of subjects' lh.thickness.fwhm15.fsaverage.mgh files to be used as input for palm. The results maps are of the .mgz format. I can convert these to .nii using mri_convert in order to use fslmaths or fslstats. My dilemma is that I'd like to use another viewing package for the palm results (i.e., Surf Ice) because of its features and some quirks I've encountered while loading results in Freeview. Surf Ice accepts a number of formats ( https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Supported_Fo…) including Freesurfer's .asc, .srf, .curv, .gcs, .pial, and .w (among *many* others), but I have yet to successfully convert these .mgz maps to a readable format. Surf Ice can read .nii, but loading my mri_converted .nii files results in a uniform surface with 0 at all vertices. Thus, I have two questions: 1) Can you think of a means to convert these surface "volumes" (.mgh/.mgz) to a desired format that can be read by Surf Ice? I've attempted mri_vol2surf, mri_surf2surf, and mris_convert, but cannot find an appropriate format/get things to work. In case it's helpful, readable formats are: 2) My alternative idea would be to instead use mri_concat on subjects' lh.thickness files and later apply fwhm smoothing. Would this approach be feasible? I could test whether pre-palm smoothed and post-palm smoothed results are equivalent, but I'm afraid that the variable dimensions of subjects' native thickness files would cause problems either with palm or when later trying to view the group-level results. Version information: Recon-all run with FreeSurfer 5.3.0 FSL 5.0.8 palm alpha112 Thank you in advance for any suggestions, and please let me know if any additional information would be helpful. With gratitude, Dan

2 1

"slides" link is not working
by Peters, Douglas G 23 Jan '19

23 Jan '19

External Email - Use Caution https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples Error Message: Not Found The requested URL /pub/docs/freesurfer.groupanalysis.short.pdf was not found on this server.

2 1

Double cursors when viewing inflated surfaces
by Bunting, Emma 23 Jan '19

23 Jan '19

External Email - Use Caution Hi, When I load my surface overlay (sig.mgh output file from GLM analysis) onto fs average lh inflated surface, I see two cursors when looking at the inner side of the brain. When i click the outer side, only one cursor shows. I have used this command to visualise the data: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:anot_outline=1:overlay=glmdir/matrix/sig.mgh:overlay_threshold=4,5 -viewport 3d I’ve worried that the labels its loading onto the brain aren'’t aligning properly if the cursor is in 2 places. Is there something wrong with my data visualisation command? Thanks in advance, Best wishes, Emma

1 0

Showing graph of freesurfer atlas
by charujing123 22 Jan '19

22 Jan '19

External Email - Use Caution Hi FS experts and users I am interested in the ROI (e.g., superiorfrontal) location on the surface. Now I only can perform this ,but this method is difficult to detect the superiorfontal region. " freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red " Thanks. Rujing 2019-01-23 charujing123

2 1

updateing freesurfer.
by Aaron Tanenbaum 22 Jan '19

22 Jan '19

External Email - Use Caution I tried updating freesurfer 6.0 using the command fs_update. I get the following output. > Build is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > Running this will update some of your freesurfer binaries. > > Shall I proceed? [y/n/Abort]: y > > rsync -zbrlv --progress --suffix=.1539713469_bak rsync:// > surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Linux-cen… > /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_6_0/ > receiving incremental file list > rsync: change_dir > "/dist/freesurfer/patches/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c" > (in pub) failed: No such file or directory (2) > > sent 8 bytes received 173 bytes 362.00 bytes/sec > total size is 0 speedup is 0.00 > rsync error: some files/attrs were not transferred (see previous errors) > (code 23) at main.c(1655) [Receiver=3.1.1] >

2 1

Version 6.1 and aseg histograms
by Hatton, Sean 22 Jan '19

22 Jan '19

External Email - Use Caution Hi all, Two quick questions: 1. Is there an expected timeframe for when FreeSurfer 6.1 (or next version) is published? 2. In aseg, is there a way to manually select the histograms or mean/SD of the ROIs? Regards, Sean Hatton, PhD Assistant Project Scientist, Center for Multimodal Imaging Genetics UCSD

2 1

nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)
by Durgerian, Sally 22 Jan '19

22 Jan '19

External Email - Use Caution Dear freesurfer team, I have been having a problem running freesurfer on one computer. The same commands and data work fine on other machines. The error message is: nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) Looking through the message board, others have had a similar problem. I have tried many of the suggestions offered without success. Note that I have the problem using freesurfer-6.0.0 as well as freesurfer-5.3.3-HCP Information on the error messages, OS and some of the things I have tried are described below. I have seen a few inquiries of this type never resolved as far as I can tell: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056844.ht… https://neurostars.org/t/fmriprep-crashing-during-freesurfer-nu-correct/2108 Anything you can suggest would be appreciated. Thanks, Sally ------------------------------------------------------------------------------------------------------------------------ I did make sure it is not a space problem:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-Februar… ------------------------------------------------------------------------------------------------------------------------ I successfully tried the minc commands which used /opt/minc/1.9.16/bin - the files were created: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-February/050030… mri_convert.bin orig.mgz orig.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig.nii... <nifti_image.../> Using s-form transform: -1.0000, 0.0000, 0.0000, 127.0000, 0.0000, 0.0000, 1.0000, -145.1500, 0.0000, -1.0000, 0.0000, 147.0000, 0.0000, 0.0000, 0.0000, 1.0000, name | start | step | cosines yspace | -145.1500 | 1.0000 | 0.0000 1.0000 0.0000 zspace | 147.0000 | -1.0000 | -0.0000 -0.0000 1.0000 xspace | 127.0000 | -1.0000 | 1.0000 -0.0000 -0.0000 mri_convert.bin junk.mnc junk.mgh $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from junk.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, -1) writing to junk.mgh... ------------------------------------------------------------------------------------------------------------------------ Here's the OS info: CentOS Linux release 7.4.1708 (Core) ------------------------------------------------------------------------------------------------------------------------ Here's the contents of recon-all.error: ------------------------------ SUBJECT FS_TEST DATE Tue Jan 22 17:07:30 GMT 2019 USER me HOST mycomputer PROCESSOR x86_64 OS Linux Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ /usr/local/freesurfer-6.0.0/bin/recon-all PWD <path to data>/FS_TEST/mri CMD mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 ------------------------------------------------------------------------------------------------------------------------ Here's the contents of FS_TEST/mri/mri_nu_correct.mni.log ------------------------------ <path to data>/FS_TEST/mri /usr/local/freesurfer-6.0.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Tue Jan 22 17:07:26 GMT 2019 Program nu_correct, built from: N3 1.12.00 tmpdir is ./tmp.mri_nu_correct.mni.81524 <path to data>/FS_TEST/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.81524/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jan 22 17:07:29 GMT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ -iterations 1000 -distance 50 Cannot read input file: ./tmp.mri_nu_correct.mni.81524/nu0.mnc [me@mycomputer:<path to data>/FS_TEST/mri/] [2019-01-22 17:07:29] running: /opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct ------------------------------------------------------------------------------------------------------------------------ ## The file that nu_correct is looking for is there: ls FS_TEST/mri/tmp.mri_nu_correct.mni.81524/nu0.mnc FS_TEST/mri/tmp.mri_nu_correct.mni.81524/nu0.mnc ------------------------------------------------------------------------------------------------------------------------ Here's the contents of FS_TEST/scripts/recon-all.log -------------------------------------------------------- Tue Jan 22 17:07:02 GMT 2019 <path to data>/FS_TEST /usr/local/freesurfer-6.0.0/bin/recon-all -i T1w_acpc_dc_restore.nii.gz -subjid FS_TEST -all subjid FS_TEST setenv SUBJECTS_DIR <path to data> FREESURFER_HOME /usr/local/freesurfer-6.0.0 Actual FREESURFER_HOME /usr/local/freesurfer-6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 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 4096 maxlocks unlimited maxsignal 514889 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131844476 1382916 504384 2483852 129957176 127079832 Swap: 4194300 226832 3967468 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: N3 1.12.00 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-6.0.0/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer-6.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### <path to data>/FS_TEST mri_convert <path to data>/T1w_acpc_dc_restore.nii.gz <path to data>/FS_TEST/mri/orig/001.mgz mri_convert.bin <path to data>/T1w_acpc_dc_restore.nii.gz <path to data>/FS_TEST/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from <path to data>/T1w_acpc_dc_restore.nii.gz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to <path to data>/FS_TEST/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Jan 22 17:07:12 GMT 2019 Found 1 runs <path to data>/FS_TEST/mri/orig/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 <path to data>/FS_TEST/mri/orig/001.mgz <path to data>/FS_TEST/mri/rawavg.mgz <path to data>/FS_TEST mri_convert <path to data>/FS_TEST/mri/rawavg.mgz <path to data>/FS_TEST/mri/orig.mgz --conform mri_convert.bin <path to data>/FS_TEST/mri/rawavg.mgz <path to data>/FS_TEST/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from <path to data>/FS_TEST/mri/rawavg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to <path to data>/FS_TEST/mri/orig.mgz... mri_add_xform_to_header -c <path to data>/FS_TEST/mri/transforms/talairach.xfm <path to data>/FS_TEST/mri/orig.mgz <path to data>/FS_TEST/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Jan 22 17:07:26 GMT 2019 <path to data>/FS_TEST/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 <path to data>/FS_TEST/mri /usr/local/freesurfer-6.0.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Tue Jan 22 17:07:26 GMT 2019 Program nu_correct, built from: N3 1.12.00 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.81524 <path to data>/FS_TEST/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.81524/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jan 22 17:07:29 GMT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ -iterations 1000 -distance 50 Cannot read input file: ./tmp.mri_nu_correct.mni.81524/nu0.mnc [me@mycomputer:<path to data>/FS_TEST/mri/] [2019-01-22 17:07:29] running: /opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FS_TEST exited with ERRORS at Tue Jan 22 17:07:30 GMT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ------------------------------------------------------------------------------------------------------------------------

1 0

LME MATHLAB tools
by Getaneh Bayu 22 Jan '19

22 Jan '19

External Email - Use Caution Dear Freesurfer Experts, I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools. I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3). I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ .... To see the difference between group g0 and group g1, I constructed the following contrast matrix using the tutorial provided in LME MATLAB tools C = [zeros(1,3) [1 0 0] zeros(1,4)]; CM.C=[zeros(1,3) [1 0 0] zeros(1,4)]; Based on the tutorial I run the following functions. rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere); F_rhstats = lme_mass_F(rhstats,CM); fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig'); nv=length(rhstats); Beta2 = zeros(1,nv); for i=1:nv if ~isempty(rhstats(i).Bhat) Beta2(i) = rhstats(i).Bhat(2); end; end; rhmri1 = rhmri; rhmri1.volsz(4) = 1; fs_write_Y(Beta2,rhmri1,'rhBeta2.mgh'); [detvtx,sided_pval,pth] = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0); fs_write_Y(sided_pval,rhmri1,'spval.mgh'); When I view sig.mgh using tksurfer I see regions with red and blue color. 1) Does the result shows the oveall change for all the five time points? 2) How do I know the difference between the two groups for each 5 time points? 3) Does red means thickness of group A is lgreater than thickness of group B? 4) what does rhBeta2.mgh and spval.mgh tell us? How can I extract the information from the file? With regards Getaneh --

1 0

← Newer
1
2
3
4
5
6
7
8
9
...
17
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer January 2019