Freesurfer

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30132 discussions

recon -all exited with errors
by Boric, Katica A. 08 Oct '13

08 Oct '13

Dear freesurfer experts: I am trying to process an MRI using recon-all -autorecon1 -autorecon2 -autorecon3 and exited with errors. Apparently the encoded image data is not supported (below you can see the recon-all.log) Is there a way to process this study? Thank you very much for your help, Katica Here is the recon-all.log: Tue Oct 8 14:06:54 PDT 2013 /home/spaz/Cat/subjects/MGH020_SurferOutput /usr/local/freesurfer/bin/recon-all -autorecon1 -autorecon2 -autorecon3 -subject MGH020_SurferOutput -i /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm subjid MGH020_SurferOutput setenv SUBJECTS_DIR /home/spaz/Cat/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 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 1024 total used free shared buffers cached Mem: 1012544 931236 81308 0 42064 556144 -/+ buffers/cache: 333028 679516 Swap: 2030588 126356 1904232 ######################################## 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: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 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: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 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: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 $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: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 $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: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:57-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:57-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:57-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/spaz/Cat/subjects/MGH020_SurferOutput mri_convert /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm /home/spaz/Cat/subjects/MGH020_SurferOutput/mri/orig/001.mgz mri_convert /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm /home/spaz/Cat/subjects/MGH020_SurferOutput/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm... Starting DICOMRead2() dcmfile = /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm dcmdir = /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3 ERROR: RLL-encoded image data not supported! (Transfer Syntax UID: 1.2.840.10008.1.2.5) Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MGH020_SurferOutput exited with ERRORS at Tue Oct 8 14:06:57 PDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1 0

mri_vol2surf clarification
by Satrajit Ghosh 08 Oct '13

08 Oct '13

hi folks, i'm using mri_vol2surf to map functional time series into fsaverage3/4. my assumption is that each vertex time series will be the mean over an icosahedral patch corresponding to the vertex on fsaverage. is that how the resampling is done? also is the resampling done with a single interpolation? if it's a single step, is there a way to project the interpolation kernel corresponding to a vertex in fsaverage3 on the subject's own surface? cheers, satra

2 2

Cluster Annotation file and mris_anatomical_stats
by Tara Ann Miskovich 08 Oct '13

08 Oct '13

Hi Everyone, I am having trouble running mris_anatomical_stats on an annotation file produced from my group analysis in qdec. This is my code, but it seems to want to pull the annotation file from the subject/label directory. Should I just make a copy into everyone's label file? mris_anatomical_stats -a qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot -t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats ${subject} lh Thank you! Tara

2 13

Re: [Freesurfer] missing eTIV in asegstats2table
by Daniel Ferreira 08 Oct '13

08 Oct '13

Dear Douglas, I generated my table with version 5.3. Attached is an example for two subjects (in .txt and .xls formats). Best regards Dani

2 1

mris_smooth issue with gaussian parameters
by Marcos Martins da Silva 08 Oct '13

08 Oct '13

Hi, Freesurfers I am getting some interesting hippocampal surfaces with the following steps: 1- recon-all -all -hippo-subfields 2- mri-concat (only CA1, CA23, CA4DG and the tail complement volumes) 3- a custom OCTAVE script to segment the concatenated volume from step 2 into Head, Body and Tail 4- mri_binarize Head, Body and Tail volumes from step 3 5- mri_tessellate the binary masks from step 4 6- mri_smooth the surfaces from step 5 Using freeview I got a screenshot showing both hippocampi segmented (hipposurf3d.png is attached). This approach worked well for 16 subjects up to step 5. Step 6 was completed as well in 13 out 16 subjects. The only problem was during left hippocampal body smoothing in 3 subjects (all the other surfaces from all 16 subjects in were smoothed with no problem). For these 3 surfaces, mris_smooth simply freezes, with no error message. I must press control + C to quit the program. During the freezing I noticed high CPU use. It follows the exactly command I used and the screen output. mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody using Gaussian curvature smoothing with norm 5.00 with 2 smooth steps averaging curvature for 1 iterations smoothing for 1 iterations smoothing surface tessellation for 1 iterations... ------------------------------------------------------ ------------------------------------------------------ ------------------ pass 1 (num=2853) ------------------ ------------------------------------------------------ ------------------------------------------------------ If I supress the gaussian parameters and run just something like: mris_smooth -nw -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody or even mris_smooth -nw surfLeftHippoBody lh.surfHippoBody I got the smoothed surface with no errors but the final quality is not as good as when I use the gaussian parameters. I am attaching one of the problematic surface files so you can check it (surfLeftHippobody). Intersting if I use a surface with all left hippocampus (including head, problematic body and tail and) smoothing completes without error Thank you very much for any help. Marcos

2 9

5.3.0, mri_segstats
by EK Kim 08 Oct '13

08 Oct '13

Dear experts, I updated FreeSurfer as a 5.3.0 version but have a problem about the missing ribbon.mgz when running recon-all procedure. I found the ftp address but couldn't find the mri_segstats. (ftp:/surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats) Could you let me know the right address of the file? Best, EK.

2 1

Problem with DWI and structural coregistration
by stdp82＠virgilio.it 08 Oct '13

08 Oct '13

Hi list, I'm performing trac-all but I'm noting some coregistration error.I have try to run separately each step. When -masks was finished, cortex masks and other file were wrongly coregistared on DTI. In the next step also the dti_FA and other maps are wrong becouse some parts are lacking. Please see also the attachments. Thanks, Stefano

1 0

half brain when converting into mgz
by Erik Lindberg 08 Oct '13

08 Oct '13

Dear Freesurfer experts, I analyzed a lot of brains in Freesurfer. For some reason some brains gets cut on the top (see attaced image). I cannot understand why this is happening. The dicom image is ok, but as soon as I convert it into mgz suddenly the top of the brain is cut off. Out of 60 brains with identical mri sequence 5 brains are cut. Would be grateful if you suggest how to solve this problem Thanks in advance! Olof

2 1

Cerebellar subdivisions
by Alan Francis 07 Oct '13

07 Oct '13

Hi Bruce et al, Is the parcellation of the cerebellar subdivisions in the works for the next version of FS? Is there an ETA for this? thanks so much, Alan

2 1

[FreeSurfer] changes to subcortical volumes
by Francesco Siciliano 07 Oct '13

07 Oct '13

Hello, After doing manual editing to the surface of a brain (brainmask.mgz, wm.mgz, and brain.finalsurfs.mgz) through freeview, I noticed that the volumes of some subcortical structures (specifically the hippocampus, amygdala, and accumbens) had changed, even though I did not edit aseg.mgz. Is that to be expected? Most of the differences were minimal, a 5% change or less. However some of the structures changed by as much as 10 or 15%. I am preparing to do a second-level analysis of ROIs of the hippocampus and amygdala on a group of subjects. Given that cortical edits seem to influence subcortical structure volumes, would it be unreliable to run a second-level analysis with subcortical volumes recorded prior to cortical editing? Thank you, -Francesco Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

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