Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

External Regressor of Interest in FS-FAST
by Mcnorgan, Christopher 11 May '16

11 May '16

The references to external regressors in mkanalysis-sess are a little sparse on how I would go about analyzing a continuous regressor: I have a mixed design experiment: TaskBlock1 Rest TaskBlock2 Rest … TaskBlockN Rest x6 Runs Within each block are jittered events (5 of condition A, 5 of condition B). A colleague of mine agreed that the A vs B contrast should be pretty robust even in a single participant (it’s an established paradigm), considering I have over 150 trials of each, but I am seeing nothing at any reasonable threshold in my single participant. My colleague suggested checking whether there were any regions with activity that increased/decreased as a function of block over the course of the experiment (essentially, a neural practice effect). Hypothetically, such a region would show a linear drift in activity across 6*N blocks, but only during the block periods (reverting to baseline during the rest periods). >From the mkanalysis-sess.new wiki page, it appears that the -extreg flag can be used to pass an additional regressor file, but it’s unclear from the rest of the description how to construct this file, nor how to view the GLM associated with this analysis. Thanks for your time; I’ll post the solution on my lab wiki once it’s all sorted out Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

1 0

Announcing the the HCP Course 2016 in Boston Aug 28-Sept 1
by Jennifer Elam 11 May '16

11 May '16

The Human Connectome Project (HCP) is pleased to announce the 2016 HCP Course: “Exploring the Human Connectome” <http://humanconnectome.org/courses/2016/exploring-the-human-connectome.php>, to be held August 28-September 1 (Sunday-Thursday) at the Joseph B. Martin Conference Center <http://www.theconfcenter.hms.harvard.edu/> at Harvard Medical School, in Boston, Massachusetts, USA. This 5-day intensive course will provide training in the acquisition, analysis and visualization of whole-brain imaging and behavioral data from the Human Connectome Project (HCP) using methods and informatics tools developed by the WU-Minn HCP consortium plus data made freely available to the neuroscience community. The course is designed for investigators who are interested in: *using data being collected and distributed by HCP *acquiring and analyzing HCP-style imaging and behavioral data at your own institution *processing your own non-HCP imaging data using HCP pipelines and methods *learning to use Connectome Workbench tools and the CIFTI connectivity data format *learning HCP multi-modal neuroimaging analysis methods, including those that combine MEG and MRI data *positioning yourself to capitalize on HCP-style data from forthcoming large-scale projects (e.g., Lifespan HCP and Connectomes Related to Human Disease) Participants will learn how to acquire, analyze, visualize, and interpret data from four major MR modalities (structural MR, resting-state fMRI, diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and extensive behavioral data. Lectures and labs will provide grounding in neurobiological as well as methodological issues involved in interpreting multimodal data, and will span the range from single-voxel/vertex to brain network analysis approaches. The course is open to graduate students, postdocs, faculty, and industry participants. The course is aimed at both new and existing users of HCP data, methods, and tools, and will cover both basic and advanced topics. Prior experience in human neuroimaging or in computational analysis of brain networks is desirable, preferably including familiarity with FSL and Freesurfer software. For more info and to register visit the HCP Course website <http://humanconnectome.org/courses/2016/exploring-the-human-connectome.php>. We hope to see you in Bah-ston! Best, 2016 HCP Course Organizers

1 0

Direction of bbregister transformation
by Michael Waskom 11 May '16

11 May '16

Hi Freesurfers, I have a question about the direction of the transformation written out to the register.dat file by bbregister. I have looked at the fscoordinates powerpoint presentation, which I think is telling me that this matrix actually maps from the orig.mgz RAS coordinates to the functional RAS coordinates. That agrees with the results I get when I try to use the matrix outside of Freesurfer. However, this is a little surprising, because I think of the bbregister process as aligning the functional (moving) with the anatomy (target) so I would have expected the transform matrix to represent that mapping. Can you please confirm whether my understanding of the fscoordinates presentation is correct, or help me out if I am off base? Thanks! Michael

2 1

Normalization for functional connectivity
by Sahil Bajaj 11 May '16

11 May '16

Hello all, I am interested in importing some seed regions which are in MNI space in order to calculate functional connectivity maps. Looks like command preproc-sess doesn't normalize the BOLD data and only the regions generated by FreeSurfer LookUp table which have 'segid', can be used to calculate functional connectivity maps. I was wondering how can I normalize the BOLD and T1w data so that I can use http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… instructions to calculate functional connectivity from MNI seed regions. Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

3 4

Correct/best way to find the midthickness surface
by Michael Waskom 11 May '16

11 May '16

Hi Freesurfers, I have seen at least three ways for identifying an intermediate surface between the white and pial surfaces: - Multiply the surface normal vector for each white surface vertex by half of the cortical thickness and add it to each vertex coordinate - Average the white and pial coordinates for each vertex - Use mris_expand, e.g. `mris_expand -thickness lh.smoothwm 0.5 lh.graymid` I have found that these approaches all give similar, but not identical results. Is there a consensus that one approach is best relative to the others? Thanks, Michael

2 1

recon-all error on ubuntu 16.04
by Mads Jensen 11 May '16

11 May '16

Dear FreeSurfer group, I get an error trying to run basic recon-all on a ubuntu 16.04 system. It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below). I have made the symbolic links from the installation notes. Any ideas or thoughts on what the problem might be or how to track it down would be very welcome. best regards, mads from bugr: FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: stretch/sid Kernel info: Linux 4.4.0-22-generic x86_64 recon-all.log: Mon May 9 11:12:07 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test /home/XYZ/Toolboxes/freesurfer/bin/recon-all -all -subjid test -i T1.mgz subjid test setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 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 62044 maxlocks unlimited maxsignal 62044 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 15924580 3455984 375968 323648 12092628 11975092 Swap: 16616956 254220 16362736 ######################################## 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: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic 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: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic 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: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic 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: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic 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: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/XYZ/Toolboxes/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/XYZ/Toolboxes/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/XYZ/Projects/tmp/fs_test/test mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/T1.mgz... TR=0.00, 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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon May 9 11:12:13 CEST 2016 Found 1 runs /home/XYZ/Projects/tmp/fs_test/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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz... TR=0.00, 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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz... mri_add_xform_to_header -c /home/XYZ/Projects/tmp/fs_test/test/mri/transforms/talairach.xfm /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon May 9 11:12:19 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s test exited with ERRORS at Mon May 9 11:12:21 CEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

3 4

QDEC - cannot allocate memory
by Marissa Pifer 11 May '16

11 May '16

Hi freesurfers, I am on a macbook pro OSX 10.9.5, trying to run an analysis on qdec - freesurfer version 5.3. I am looking to analyze T2weighted scans for 27 subjects through the qdec system. I keep getting this error that it cannot allocate memory for the task. I'v been talking with our IT people and they've told me I have more than enough space on the computer, so it must be an issue with the program or how it's set up. This is the error message: *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes! Cannot allocate memory Does anyone know what I can do to fix this problem? Thanks, Marissa

3 6

cerebellar surface
by Alexopoulos, Dimitrios 11 May '16

11 May '16

Hi all, Freesurfer generates a volumetric parcellation of the cerebellum, but is there a method to generate the surface reconstruction, or perhaps just a hull surface from freesurfer output. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.

4 6

Manual segmentation issues
by Saturne Fox 11 May '16

11 May '16

Dear freesurfer users community, I need your help concerning manual segmentation issues.

2 7

GLM - covariate question
by Pedro Rosa 10 May '16

10 May '16

Dear list, I am running a command line group analysis, and I want to include a covariate that is zero for all subjects in a group, and diverse for all subjects in the second group (medication intake, which is null for all subjects in the control group). This generates a lack of range of that continuous variable within a class (control group), and thus mri_glmfit ends with errors. Is it possible to perform such analysis? Could demeaning procedure work here? If not, how could I "regress out" the effect of such covariate in between-groups thickness/area differences? Many thanks in advance, Pedro.

2 2

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