Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

make_average_subject monkey data
by Francesca Strappini 16 Mar '18

16 Mar '18

Dear Experts, I'm trying to average two monkey brains. I run this command line: make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkeys but it ended with errors. I run the recon-all for both monkyes with the option -notal-check because I had problems with the Talairach registration. I don't know if this could be the cause. Thanks a lot Francesca Tue Mar 13 20:04:06 CET 2018 /usr/local/freesurfer/subjects/AVGmonkeys /usr/local/freesurfer/bin/recon-all -s AVGmonkeys -cortribbon -aparc2aseg subjid AVGmonkeys setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 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 63682 maxlocks unlimited maxsignal 63682 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16350220 4943572 7520800 278988 3885848 10739864 Swap: 19528700 0 19528700 ######################################## 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: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic 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: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic 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: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic 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: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/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/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Cortical ribbon mask Tue Mar 13 20:04:06 CET 2018 /usr/local/freesurfer/subjects/AVGmonkeys/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AVGmonkeys SUBJECTS_DIR is /usr/local/freesurfer/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 34535 writing volume /usr/local/freesurfer/subjects/AVGmonkeys/mri/ribbon.mgz ERROR: ribbon has non-zero value at location 0,0,0 Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AVGmonkeys exited with ERRORS at Tue Mar 13 20:26:58 CET 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

3 8

Mean baseline Cth for each subject in a cluster obtained from a spc analysis
by Fred Sampedro 16 Mar '18

16 Mar '18

Dear Freesurfer Experts, I ran a longitudinal Cth analysis and found a cluster with significant spc differences between two groups. It was easy to obtain the mean spc values in that cluster for all the subjects. However, I would also like to have a spreedsheet with the baseline mean Cth values in that cluster for all my subjects to correlate with other clinical measures. My attempt was: mri_segstats --i SPC_ANALYSIS_FOLDER/y.mgh --seg SPC_ANALYSIS_FOLDER/SUBANALYSIS/mc-z.abs.th13.sig.cluster.mgh --excludeid 0 --sum CTH_inSPC_cluster.sum But obviously this is not the correct way to obtain for each subject the mean Cth value in that cluster. Any help would be much appreciated! Thanks a lot in advance, Fred

2 1

Map mask from volume to surface for small volume correction in surface analyses (using my own template)
by Charlotte Grosse Wiesmann 16 Mar '18

16 Mar '18

Dear freesurfer experts, I would like to restrict my surface analyses (cortical thickness and surface area) to a mask from an fMRI meta-analysis using my own subject-specific template that I created with ANTS. So far, I have used Qdec and wanted to correct for cluster size running the Monte Carlo (MC) simulation on my own template. Now I would like to restrict the simulation to my mask to do a small volume correction in my regions of interest. I mapped the mask to my own template (in volume space) using ANTS (WarpImageMultiTransform) but how can I get this mask to the surface space to run the MC simulation on my own template within this mask? I was planning to do: mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z --surface my_template ?h --nreps 10000 --mask mymask.mgz How do I get mymask.mgz in the correct space for this? And can I continue using Qdec or do I have to use glmfit for these analyses? In addition: is it also possible to do a small volume correction using FDR rather than cluster-size correction? Thanks for your help! Charlotte

3 6

Postdoctoral Fellow Position at the University of Pittsburgh
by Cat Camacho 15 Mar '18

15 Mar '18

Hello fellow neuroimagers! The Laboratory for Child Brain Development at the University of Pittsburgh is looking for a postdoctoral fellow starting this summer or fall. The LCBD employs multimodal neuroimaging to study child affective development from infancy to middle childhood. Please see the attached ad for more information. Thanks! Cat -- Maria Catalina Camacho PhD Student Center for Neuroscience Laboratory for Child Brain Development University of Pittsburgh mccamacho(a)pitt.edu 512-591-3741

1 0

Skull stripping error dataset
by Matthew Grecsek 15 Mar '18

15 Mar '18

I uploaded the datasets to the ftp site, does anyone have further advice regarding this issue? Both datasets are for the same subject for a longitudinal concussion study and fail for different reasons. matt1 - has "ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 errors" and fails with "CORRECTING DEFECT 51 (vertices=28380, convex hull=5261, v0=32826) XL defect detected..." never completing. matt2 - is leaving out large sections of brain despite various wsthresh adjustments (see thread below) I appreciate any assistance you can provide. All the best, -Matt Hi Matt no idea what that would happen. If you upload the dataset we will take a look cheers Bruce On Mon, 5 Mar 2018, Matthew Grecsek wrote: Following your advice below, it was clearly apparent that the output from the skull stripping step was missing a lot. I tried adjusting the -wsthresh flag from 50 -> 200 and it still left major parts of the brain out. I have a good quality mri and subject with no known anatomical abnormalities. The log file indicates "surface validation has detected possible Error" Does this suggest a more meaningful defect in the base image or something that can be corrected via other parameters or manual editing? Log file attached. Thanks, -Matt Bruce Fischl Fri, 02 Mar 2018 08:00:11 -0800 Hi Matt check the output of the skull stripping. This error usually means that too much (everything?) has been erased and no plausible cc could be found cheers Bruce On Thu, 1 Mar 2018, Matthew Grecsek wrote: My recon-all ended prematurely with the following message: final transformation (x=136.0, yr=-10.054, zr=-0.114): 0.98464 0.00200 -0.17457 15.51372; -0.00197 1.00000 0.00035 17.22442; 0.17457 0.00000 0.98464 -17.83761; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping No such file or directory Linux centos-7-1 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 matt2 exited with ERRORS at Thu Mar 1 04:35:09 UTC 2018 I am running: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c My full log file is attached. Please let me know suggestions for correcting and continuing the process. Thanks, -Matt

1 0

Re: [Freesurfer] Using .label file as mask in mri_fdr
by Chen Jen-I. 15 Mar '18

15 Mar '18

This is surface-based analysis. I used tksurfer to load the mask.mgh as overlay e.g. tksurfer fsaverage rh inflated -fthresh 2.3 -overlay mask.mgh -delink -curv -gray The mask.mgh file is from the GLMFIT folder after I ran mri_glmfit on my cortical thickness data within the areas set by the label that I have specified Thanks. Jeni Chen Douglas N. Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Wed, 14 Mar 2018 15:32:51 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Is this a volume or surface-based analysis? How did you try to visualize it? On Mar 10, 2018, at 12:56 AM, Chen Jen-I. <jen-i.chen(a)umontreal.ca<mailto:jen-i.chen@umontreal.ca>> wrote: Hello, I want to do a FDR correction using mri_fdr within a ROI mask (in .label format). I see the option of passing the sig.mgh volume through a mask, and I read that one can use the mask.mgh in the GLMFIT folder. What is this mask.mgh? I tried to visualize it in Freeview but it doesn’t look like a mask but rather some sort of geometric form. If I have labels as my ROI, how do I convert that into a .mgh format to be used in mri_fdr? (I tried simply using the label file first and obviously that didn’t work…) Thank you in advance, Jeni Chen

2 1

Registering functional data between scan sessions
by David Beeler 15 Mar '18

15 Mar '18

Hi, I have some functional data for the same localizer (dimensions 80x80x38x246) that was acquired in the same subject on two separate days. I would like day 1's raw data to be spatially aligned to the anatomical taken on day 2, but still have the low resolution dimensions of functional space. This question has been asked a couple times before in various forms, but I can't seem to find a clear answer of how to do this correctly. Anatomicals were collected on both days, so I figured I could do something like this: mri_vol2vol --nearest --regheader --mov day1-f.nii.gz --targ $SUBJECTS_DIR/S03/mri/brain.mgz --o day1-f-in-day1-3danat.nii.gz bbregister --s S03_day1 --mov $SUBJECTS_DIR/S03_day2/mri/brain.mgz --reg day1-to-day2.lta --init-fsl --t1 mri_vol2vol --mov $SUBJECTS_DIR/S03_day2/mri/brain.mgz --targ day1-f-in-day1-3danat.nii.gz --o day1-f-in-day2-3danat.nii.gz --reg day1-to-day2.lta --nearest --inv mri_vol2vol --regheader --mov day1-f-in-day2-3danat.nii.gz --targ day2-f.nii.gz --o day1-f-in-day2-func.nii.gz but this is a bad solution because I shouldn't have to actually upsample every time point to high resolution space and then back down again. I figure there must be a way to use the --no-resample flag of mri_vol2vol or something to keep the voxel number (relatively) low and just use the transformation matrix information to go straight from day 1 functional to day 2 functional. Let me know if you have any ideas, thanks! David

2 1

Re: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0
by Alexopoulos, Dimitrios 15 Mar '18

15 Mar '18

The command below appears to have run successfully but I get a note that the 'volumesAmygdla.txt' file could not be moved. See message below at the end of the freesurfer run. I am using 6.0 (Jan. 18, 2017 release). Is this expected? Jim ----------------------------------------------------------------------- Not resampling, only changing vox2ras matrix To check registration, run: tkregister2 --mov T2inT1space.mgz --targ /data/nil-bluearc/shimony/neonatal/wunder_9_10yo/freesurfer6_0/processed_data/neo321e_fs/mri/norm.mgz --regheader --reg /tmp/reg mri_vol2vol done mv: cannot stat 'volumesAmygdala.txt': No such file or directory Everything done! It took 1921.1425 seconds Started at Wed Mar 14 17:04:06 CDT 2018 Ended at Thu Mar 15 05:35:24 CDT 2018 #@#%# recon-all-run-time-hours 12.522 recon-all -s neo321e_fs finished without error at Thu Mar 15 05:35:24 CDT 2018 done jimalex@linux1% From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Tuesday, March 13, 2018 3:22 AM To: freesurfer(a)nmr.mgh.harvard.edu; Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0 Looks good to me! Sent from my phone, please excuse brevity and typos ________________________________ From: 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>> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos(a)wustl.edu<mailto:dimitriosalexopoulos@wustl.edu>> Sent: Tuesday, March 13, 2018 1:06:25 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0 I need a clarification with the command to run for generating the hippo subfields on 6.0 using both a T1 mprage and T2 space (both 1mm isotropic). I'd like to run the entire recon-all -all surface and hippo subfields processing stream. Would this be the correct command: recon-all -s subject -i dicom.dcm -hippocampal-subfields-T1T2 T2.nii.gz T1T2 -all Thanks. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

Installation problem
by Neda Mohammadi 15 Mar '18

15 Mar '18

Dear Expert, I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps: 1. Download and extract into the directory /usr/local 2.export FREESURFER_HOME=/usr/local/freesurfer Its fine, but when I run this step 3.source $FREESURFER_HOME/SetUpFreeSurfer.sh I receive this message n time -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Work/Processed_data/freesurfer MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 and I must press Ctrl+C to stop. What do I do now? -- *Best Regards,* *Neda*

2 3

lh.volume not found
by Maria Carla Piastra 14 Mar '18

14 Mar '18

Dear Freesurfers, I am running the pipeline described here: http://www.fieldtriptoolbox.org/tutorial/sourcemodel and it fails: mris_convert --volume Subject01_fieldtrip lh /DATA2/results_freesurfer/Subject01/surf/lh.volume MRISread(/DATA2/results_freesurfer/Subject01/surf/lh.white): could not open file No such file or directory when running: /recon-all -finalsurfs -subjid Subject01/ lh.volume does not exist so far. How can I create it? I tried to follow the suggestion here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06716.html, without success. Many thanks, Maria Carla

2 1

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