Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Help with freeview on Mac OS X
by Ginsburg, Daniel 28 Dec '09

28 Dec '09

Hi All, I am attempting to build and run freeview on Mac OS X 10.6.1 and am having problems with freeview crashing on startup. From gdb, the crash is the following: Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_PROTECTION_FAILURE at address: 0x00000000 0x00000000 in ?? () (gdb) backtrace #0 0x00000000 in ?? () #1 0x02b148c0 in vtkOpenGLRenderWindow::OpenGLInit () #2 0x02b391a9 in vtkCarbonRenderWindow::CreateAWindow () #3 0x02b37fa4 in vtkCarbonRenderWindow::WindowInitialize () #4 0x02b36435 in vtkCarbonRenderWindow::Start () #5 0x02a9d1db in vtkRenderWindow::DoStereoRender () #6 0x02a9d3a9 in vtkRenderWindow::DoFDRender () #7 0x02a9d832 in vtkRenderWindow::DoAARender () #8 0x02a9bc54 in vtkRenderWindow::Render () #9 0x00130417 in wxVTKRenderWindowInteractor::OnPaint (this=0x1d05aa00) at wxVTKRenderWindowInteractor.cpp:409 I am on Mac OS X 10.6.1 and build the freesurfer tree using the following settings: CFLAGS=-m32 CXXFLAGS=-m32 LDFLAGS=-m32 ./configure --disable-Wall --disable-Werror --prefix=/chb/freesurfer/ x86_64-Darwin/packages/freesurfer/dev/ --with-wxwidgets-dir=/usr/pubsw/ packages/wxWidgets/wxMac-2.8.10/ I have the /usr/pubsw tree mapped to /space/lyon/9/pubsw/MacOS10.5- i686 on the NMR network (for what it's worth, I have also tried building all of freesurfer with all of the dependent libraries installed locally and ran into the same issue). When I try running the same executable on a Mac OS X 10.5.8 machine I get the following different error: LSOpenFromURLSpec() failed with error -10810 for the file /chb/ freesurfer/x86_64-Darwin/packages/freesurfer/dev/bin/Freeview.app. I have not had any luck resolving the errors on either system. Some help from someone who has successfully run freeview on the Mac would be greatly appreciated. Thank you! -- Dan

1 0

Talairach on Non-human Primates
by Matt Glasser 28 Dec '09

28 Dec '09

I am wondering if it is necessary to perform the taltransform (or care about the results when it fails) to get good surfaces of non-human primate brains? I know I can go in and manually edit it to get it right, but I would rather not do this if it isn't critical for surface generation. Is it okay to just use -notalcheck and ignore any errors? My brains are already AC/PC aligned in a non-human primate specific standard space. Thanks, Matt.

3 6

make_average_subject error
by Estephan Moana 23 Dec '09

23 Dec '09

I am trying to make a group average of 5 subjects using the make_average_subject command - All subjects have cortical reconstruction done using recon-all. I attached the log file here, and the last few line reads: ----------------------- mri_concat ./tmp.mris_preproc.18803/20080724_N005/.1.mgh ./tmp.mris_preproc.18803/20080729_N002/.2.mgh ./tmp.mris_preproc.18803/20080729_N004/.3.mgh ./tmp.mris_preproc.18803/20080729_N004/.4.mgh ./tmp.mris_preproc.18803/20080807_N003/.5.mgh --o rh.orig.avg.area.mgh --mean mghRead(./tmp.mris_preproc.18803/20080724_N005/.1.mgh, -1): could not open file ninputs = 5 Checking inputs ERROR: reading ./tmp.mris_preproc.18803/20080724_N005/.1.mgh Any ideas what may be wrong? The one thing I can think of is that recon-all was ran locally in Freesurfer 4.4.0 while I am trying to run make_average_subject in a computer-cluster that has version 4.2.0. Can this be the problem here? Estephan Job <make_average_surface --subjects 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ --out AO_fMRI_average> was submitted from host <bc16-n13> by user <moana> in cluster <lucky>. Job was executed on host(s) <bc01-n14>, in queue <week>, as user <moana> in cluster <lucky>. </afs/isis.unc.edu/home/m/o/moana> was used as the home directory. </largefs/moana/AO_fMRI/FreeSurfer_analysis_valid> was used as the working directory. Started at Tue Dec 22 23:12:17 2009 Results reported at Tue Dec 22 23:22:05 2009 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input make_average_surface --subjects 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ --out AO_fMRI_average ------------------------------------------------------------ Exited with exit code 1. Resource usage summary: CPU time : 568.38 sec. Max Memory : 342 MB Max Swap : 837 MB Max Processes : 9 Max Threads : 9 The output (if any) follows: Your home directory for this job is /netscr/moana $Id: make_average_surface,v 1.39.2.1 2007/10/16 15:49:52 nicks Exp $ Tue Dec 22 23:12:17 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid setenv SUBJECTS_DIR /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid output ddir is /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid uid=158947(moana) gid=203(graduate) groups=203(graduate) context=root:system_r:unconfined_t:SystemLow-SystemHigh ==================== make_average_surface ==================== Tue Dec 22 23:12:17 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid /afs/isis/pkg/freesurfer-420/freesurfer64/bin/make_average_surface --subjects 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ --out AO_fMRI_average input subjects: 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ output subject: AO_fMRI_average mri_add_xform_to_header -c auto /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/mri/mni305.cor.mgz /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/mri/mni305.cor.mgz INFO: extension is mgz #@# Making lh annotation --------------------- Tue Dec 22 23:12:19 EST 2009 mris_ca_label -ml-annot lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs 7 label/lh.aparc.annot /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average ML Label: lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs 7 label/lh.aparc.annot Reading icosahedron /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri Reading gcsa from /afs/isis/pkg/freesurfer-420/freesurfer64/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs reading color table from GCSA file.... average std = 2.1 using min determinant for regularization = 0.044 0 singular and 372 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 378 changed) writing colortable into annotation file... mris_ca_label -ml-annot lh.atlas2005_simple.gcs 7 label/lh.aparc.a2005s.annot /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average ML Label: lh.atlas2005_simple.gcs 7 label/lh.aparc.a2005s.annot Reading icosahedron /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri Reading gcsa from /afs/isis/pkg/freesurfer-420/freesurfer64/average/lh.atlas2005_simple.gcs reading color table from GCSA file.... average std = 4.5 0.2 using min determinant for regularization = 0.000 0 singular and 1215 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 1804 changed) writing colortable into annotation file... #@# Making average lh.orig surface --------------------- Tue Dec 22 23:12:29 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_make_average_surface -i 7 -o orig -sdir-out /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid lh orig_avg sphere.reg AO_fMRI_average 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ reading vertex positions from orig... --------------------------------------------------- hemi = lh avg_surf_name = orig_avg canon_surf_name = sphere.reg out_sname = AO_fMRI_average xform = talairach.xfm --------------------------------------------------- --------------------------------------------------- #@# processing subject 1/5 20080724_N005/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//mri/T1.mgz Surface area: 796.5 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 2/5 20080729_N002/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//mri/T1.mgz Surface area: 821.0 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 3/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 852.6 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 4/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 852.6 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 5/5 20080807_N003/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//mri/T1.mgz Surface area: 888.3 cm2 Applying linear transform Finished loading all data Avg surf area = 842.209 cm Reading icosahedron from /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri... setting group surface area to be 842.2 cm2 (scale=0.97) writing average orig_avg surface to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.orig_avg writing group avg surface area 842 cm2 into surface file mris_make_average_surface done #@# Making average lh.white surface --------------------- Tue Dec 22 23:13:01 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_make_average_surface -i 7 -o white -sdir-out /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid lh white_avg sphere.reg AO_fMRI_average 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ reading vertex positions from white... --------------------------------------------------- hemi = lh avg_surf_name = white_avg canon_surf_name = sphere.reg out_sname = AO_fMRI_average xform = talairach.xfm --------------------------------------------------- --------------------------------------------------- #@# processing subject 1/5 20080724_N005/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//mri/T1.mgz Surface area: 831.4 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 2/5 20080729_N002/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//mri/T1.mgz Surface area: 832.6 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 3/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 879.2 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 4/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 879.2 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 5/5 20080807_N003/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//mri/T1.mgz Surface area: 913.6 cm2 Applying linear transform Finished loading all data Avg surf area = 867.199 cm Reading icosahedron from /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri... setting group surface area to be 867.2 cm2 (scale=0.97) writing average white_avg surface to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.white_avg writing group avg surface area 867 cm2 into surface file mris_make_average_surface done #@# Making average lh.pial surface --------------------- Tue Dec 22 23:13:26 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_make_average_surface -i 7 -o pial -sdir-out /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid lh pial_avg sphere.reg AO_fMRI_average 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ reading vertex positions from pial... --------------------------------------------------- hemi = lh avg_surf_name = pial_avg canon_surf_name = sphere.reg out_sname = AO_fMRI_average xform = talairach.xfm --------------------------------------------------- --------------------------------------------------- #@# processing subject 1/5 20080724_N005/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//mri/T1.mgz Surface area: 987.8 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 2/5 20080729_N002/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//mri/T1.mgz Surface area: 968.1 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 3/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 1026.0 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 4/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 1026.0 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 5/5 20080807_N003/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//mri/T1.mgz Surface area: 1074.9 cm2 Applying linear transform Finished loading all data Avg surf area = 1016.56 cm Reading icosahedron from /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri... setting group surface area to be 1016.6 cm2 (scale=0.98) writing average pial_avg surface to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.pial_avg writing group avg surface area 1017 cm2 into surface file mris_make_average_surface done #@# Making average lh.inflated surface --------------------- Tue Dec 22 23:13:52 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_make_average_surface -i 7 -o inflated -sdir-out /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid lh inflated_avg sphere.reg AO_fMRI_average 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ reading vertex positions from inflated... --------------------------------------------------- hemi = lh avg_surf_name = inflated_avg canon_surf_name = sphere.reg out_sname = AO_fMRI_average xform = talairach.xfm --------------------------------------------------- --------------------------------------------------- #@# processing subject 1/5 20080724_N005/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//mri/T1.mgz Surface area: 758.4 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 2/5 20080729_N002/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//mri/T1.mgz Surface area: 754.7 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 3/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 799.8 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 4/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 799.8 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 5/5 20080807_N003/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/lh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//mri/T1.mgz Surface area: 829.9 cm2 Applying linear transform Finished loading all data Avg surf area = 788.544 cm Reading icosahedron from /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri... setting group surface area to be 788.5 cm2 (scale=0.85) writing average inflated_avg surface to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.inflated_avg writing group avg surface area 789 cm2 into surface file mris_make_average_surface done --------------------------------------------------- #@# Making average lh.sulc ---------------------- Tue Dec 22 23:14:18 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_average_curvature -o AO_fMRI_average sulc lh sphere.reg 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.avg_sulc painting output onto subject AO_fMRI_average. processing subject 20080724_N005/... processing subject 20080729_N002/... processing subject 20080729_N004/... processing subject 20080729_N004/... processing subject 20080807_N003/... reading output surface /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.sphere.reg... #@# Making average lh.curv ---------------------- Tue Dec 22 23:14:30 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_average_curvature -o AO_fMRI_average curv lh sphere.reg 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.avg_curv painting output onto subject AO_fMRI_average. processing subject 20080724_N005/... processing subject 20080729_N002/... processing subject 20080729_N004/... processing subject 20080729_N004/... processing subject 20080807_N003/... reading output surface /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.sphere.reg... #@# Making average lh.thickness ---------------------- Tue Dec 22 23:14:43 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_average_curvature -o AO_fMRI_average thickness lh sphere.reg 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.avg_thickness painting output onto subject AO_fMRI_average. processing subject 20080724_N005/... processing subject 20080729_N002/... processing subject 20080729_N004/... processing subject 20080729_N004/... processing subject 20080807_N003/... reading output surface /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.sphere.reg... --------------------------------------------------- #@# Smoothing, inflating, etc lh ---------------- /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf mris_smooth smoothing for 5 iterations reading group avg surface area 867 cm2 from file smoothing surface tessellation for 5 iterations... smoothing complete - recomputing first and second fundamental forms... writing smoothed curvature to ./lh.curv writing smoothed area to ./lh.area writing group avg surface area 867 cm2 into surface file mris_inflate reading group avg surface area 867 cm2 from file avg radius = 50.9 mm, total surface area = 84883 mm2 writing inflated surface to ./lh.inflated writing sulcal depths to ./lh.sulc step 000: RMS=0.066 (target=0.015) step 005: RMS=0.049 (target=0.015) step 010: RMS=0.039 (target=0.015) step 015: RMS=0.032 (target=0.015) step 020: RMS=0.026 (target=0.015) step 025: RMS=0.022 (target=0.015) step 030: RMS=0.019 (target=0.015) step 035: RMS=0.016 (target=0.015) inflation complete. writing group avg surface area 867 cm2 into surface file inflation took 1.4 minutes mris_curvature averaging curvature patterns 10 times. reading group avg surface area 867 cm2 from file total integrated curvature = -71.149*4pi (-894.090) --> 72 handles ICI = 343.3, FI = 5231.0, variation=78141.753 writing Gaussian curvature to ./lh.white_avg.K...done. writing mean curvature to ./lh.white_avg.H...done. mri_annotation2label --subject AO_fMRI_average --hemi lh --outdir /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078 --annotation aparc.a2005s reading group avg surface area 867 cm2 from file reading colortable from annotation file... colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2005.txt) subject = AO_fMRI_average annotation = aparc.a2005s hemi = lh outdir = (null) surface = white Reading surface /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/lh.white Loading annotations from /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/label/lh.aparc.a2005s.annot max index = 81 3 395 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_cingulate-Isthmus.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_cingulate-Isthmus.label 4 2861 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_cingulate-Main_part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_cingulate-Main_part.label 5 1479 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_cuneus.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_cuneus.label 6 1838 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_frontal_inf-Opercular_part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_frontal_inf-Opercular_part.label 7 462 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_frontal_inf-Orbital_part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_frontal_inf-Orbital_part.label 8 1048 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_frontal_inf-Triangular_part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_frontal_inf-Triangular_part.label 9 3827 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.G_frontal_middle.label LabelWrite: 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/largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_cingulate-Main_part_and_Intracingulate.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_cingulate-Main_part_and_Intracingulate.label 48 1553 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_cingulate-Marginalis_part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_cingulate-Marginalis_part.label 49 843 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_circular_insula_anterior.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_circular_insula_anterior.label 50 2214 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/largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_orbital_medial-Or_olfactory.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_orbital_medial-Or_olfactory.label 68 293 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_paracentral.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_paracentral.label 69 2208 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_parieto_occipital.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_parieto_occipital.label 70 2269 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_pericallosal.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_pericallosal.label 71 4420 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_postcentral.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_postcentral.label 72 1938 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_precentral-Inferior-part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_precentral-Inferior-part.label 73 1902 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_precentral-Superior-part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_precentral-Superior-part.label 74 71 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_subcentral_ant.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_subcentral_ant.label 75 263 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_subcentral_post.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_subcentral_post.label 76 493 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_suborbital.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_suborbital.label 77 1446 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_subparietal.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_subparietal.label 79 1304 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_temporal_inferior.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_temporal_inferior.label 80 6746 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_temporal_superior.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_temporal_superior.label 81 474 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_temporal_transverse.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/lh.S_temporal_transverse.label mri_mergelabels -o /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/label/lh.cortex.label -d /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078 Done #@# Making rh annotation --------------------- Tue Dec 22 23:16:46 EST 2009 mris_ca_label -ml-annot rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs 7 label/rh.aparc.annot /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average ML Label: rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs 7 label/rh.aparc.annot Reading icosahedron /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri Reading gcsa from /afs/isis/pkg/freesurfer-420/freesurfer64/average/rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 318 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 328 changed) writing colortable into annotation file... mris_ca_label -ml-annot rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average ML Label: rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot Reading icosahedron /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri Reading gcsa from /afs/isis/pkg/freesurfer-420/freesurfer64/average/rh.atlas2005_simple.gcs reading color table from GCSA file.... average std = 1.0 0.2 using min determinant for regularization = 0.000 0 singular and 827 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 1935 changed) writing colortable into annotation file... #@# Making average rh.orig surface --------------------- Tue Dec 22 23:16:56 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_make_average_surface -i 7 -o orig -sdir-out /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid rh orig_avg sphere.reg AO_fMRI_average 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ reading vertex positions from orig... --------------------------------------------------- hemi = rh avg_surf_name = orig_avg canon_surf_name = sphere.reg out_sname = AO_fMRI_average xform = talairach.xfm --------------------------------------------------- --------------------------------------------------- #@# processing subject 1/5 20080724_N005/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//mri/T1.mgz Surface area: 791.1 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 2/5 20080729_N002/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//mri/T1.mgz Surface area: 810.2 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 3/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 835.8 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 4/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 835.8 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 5/5 20080807_N003/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//mri/T1.mgz Surface area: 872.7 cm2 Applying linear transform Finished loading all data Avg surf area = 829.09 cm Reading icosahedron from /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri... setting group surface area to be 829.1 cm2 (scale=0.97) writing average orig_avg surface to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.orig_avg writing group avg surface area 829 cm2 into surface file mris_make_average_surface done #@# Making average rh.white surface --------------------- Tue Dec 22 23:17:22 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_make_average_surface -i 7 -o white -sdir-out /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid rh white_avg sphere.reg AO_fMRI_average 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ reading vertex positions from white... --------------------------------------------------- hemi = rh avg_surf_name = white_avg canon_surf_name = sphere.reg out_sname = AO_fMRI_average xform = talairach.xfm --------------------------------------------------- --------------------------------------------------- #@# processing subject 1/5 20080724_N005/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//mri/T1.mgz Surface area: 824.5 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 2/5 20080729_N002/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//mri/T1.mgz Surface area: 832.0 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 3/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 863.3 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 4/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 863.3 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 5/5 20080807_N003/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//mri/T1.mgz Surface area: 895.5 cm2 Applying linear transform Finished loading all data Avg surf area = 855.726 cm Reading icosahedron from /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri... setting group surface area to be 855.7 cm2 (scale=0.97) writing average white_avg surface to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.white_avg writing group avg surface area 856 cm2 into surface file mris_make_average_surface done #@# Making average rh.pial surface --------------------- Tue Dec 22 23:17:46 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_make_average_surface -i 7 -o pial -sdir-out /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid rh pial_avg sphere.reg AO_fMRI_average 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ reading vertex positions from pial... --------------------------------------------------- hemi = rh avg_surf_name = pial_avg canon_surf_name = sphere.reg out_sname = AO_fMRI_average xform = talairach.xfm --------------------------------------------------- --------------------------------------------------- #@# processing subject 1/5 20080724_N005/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//mri/T1.mgz Surface area: 988.4 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 2/5 20080729_N002/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//mri/T1.mgz Surface area: 966.5 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 3/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 1008.5 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 4/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 1008.5 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 5/5 20080807_N003/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//mri/T1.mgz Surface area: 1048.4 cm2 Applying linear transform Finished loading all data Avg surf area = 1004.08 cm Reading icosahedron from /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri... setting group surface area to be 1004.1 cm2 (scale=0.98) writing average pial_avg surface to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.pial_avg writing group avg surface area 1004 cm2 into surface file mris_make_average_surface done #@# Making average rh.inflated surface --------------------- Tue Dec 22 23:18:11 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_make_average_surface -i 7 -o inflated -sdir-out /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid rh inflated_avg sphere.reg AO_fMRI_average 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ reading vertex positions from inflated... --------------------------------------------------- hemi = rh avg_surf_name = inflated_avg canon_surf_name = sphere.reg out_sname = AO_fMRI_average xform = talairach.xfm --------------------------------------------------- --------------------------------------------------- #@# processing subject 1/5 20080724_N005/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//mri/T1.mgz Surface area: 750.5 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 2/5 20080729_N002/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//mri/T1.mgz Surface area: 752.9 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 3/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 783.9 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 4/5 20080729_N004/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//mri/T1.mgz Surface area: 783.9 cm2 Applying linear transform --------------------------------------------------- #@# processing subject 5/5 20080807_N003/... Reading /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/rh.sphere.reg Read /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//mri/T1.mgz Surface area: 814.9 cm2 Applying linear transform Finished loading all data Avg surf area = 777.186 cm Reading icosahedron from /afs/isis/pkg/freesurfer-420/freesurfer64/lib/bem/ic7.tri... setting group surface area to be 777.2 cm2 (scale=0.85) writing average inflated_avg surface to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.inflated_avg writing group avg surface area 777 cm2 into surface file mris_make_average_surface done --------------------------------------------------- #@# Making average rh.sulc ---------------------- Tue Dec 22 23:18:36 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_average_curvature -o AO_fMRI_average sulc rh sphere.reg 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.avg_sulc painting output onto subject AO_fMRI_average. processing subject 20080724_N005/... processing subject 20080729_N002/... processing subject 20080729_N004/... processing subject 20080729_N004/... processing subject 20080807_N003/... reading output surface /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.sphere.reg... #@# Making average rh.curv ---------------------- Tue Dec 22 23:18:49 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_average_curvature -o AO_fMRI_average curv rh sphere.reg 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.avg_curv painting output onto subject AO_fMRI_average. processing subject 20080724_N005/... processing subject 20080729_N002/... processing subject 20080729_N004/... processing subject 20080729_N004/... processing subject 20080807_N003/... reading output surface /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.sphere.reg... #@# Making average rh.thickness ---------------------- Tue Dec 22 23:19:01 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average mris_average_curvature -o AO_fMRI_average thickness rh sphere.reg 20080724_N005/ 20080729_N002/ 20080729_N004/ 20080729_N004/ 20080807_N003/ /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.avg_thickness painting output onto subject AO_fMRI_average. processing subject 20080724_N005/... processing subject 20080729_N002/... processing subject 20080729_N004/... processing subject 20080729_N004/... processing subject 20080807_N003/... reading output surface /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.sphere.reg... --------------------------------------------------- #@# Smoothing, inflating, etc rh ---------------- /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf mris_smooth smoothing for 5 iterations reading group avg surface area 856 cm2 from file smoothing surface tessellation for 5 iterations... smoothing complete - recomputing first and second fundamental forms... writing smoothed curvature to ./rh.curv writing smoothed area to ./rh.area writing group avg surface area 856 cm2 into surface file mris_inflate reading group avg surface area 856 cm2 from file avg radius = 50.4 mm, total surface area = 83219 mm2 writing inflated surface to ./rh.inflated writing sulcal depths to ./rh.sulc step 000: RMS=0.066 (target=0.015) step 005: RMS=0.049 (target=0.015) step 010: RMS=0.039 (target=0.015) step 015: RMS=0.032 (target=0.015) step 020: RMS=0.027 (target=0.015) step 025: RMS=0.023 (target=0.015) step 030: RMS=0.019 (target=0.015) step 035: RMS=0.017 (target=0.015) inflation complete. writing group avg surface area 856 cm2 into surface file inflation took 1.4 minutes mris_curvature averaging curvature patterns 10 times. reading group avg surface area 856 cm2 from file total integrated curvature = -60.616*4pi (-761.720) --> 62 handles ICI = 466.4, FI = 11983.4, variation=166517.028 writing Gaussian curvature to ./rh.white_avg.K...done. writing mean curvature to ./rh.white_avg.H...done. mri_annotation2label --subject AO_fMRI_average --hemi rh --outdir /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078 --annotation aparc.a2005s reading group avg surface area 856 cm2 from file reading colortable from annotation file... colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2005.txt) subject = AO_fMRI_average annotation = aparc.a2005s hemi = rh outdir = (null) surface = white Reading surface /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.white Loading annotations from /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/label/rh.aparc.a2005s.annot max index = 81 3 387 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_cingulate-Isthmus.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_cingulate-Isthmus.label 4 2350 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_cingulate-Main_part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_cingulate-Main_part.label 5 1412 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_cuneus.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_cuneus.label 6 1479 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_inf-Opercular_part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_inf-Opercular_part.label 7 380 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_inf-Orbital_part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_inf-Orbital_part.label 8 1117 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_inf-Triangular_part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_inf-Triangular_part.label 9 4099 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_middle.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_middle.label 10 7949 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_superior.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontal_superior.label 11 383 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontomarginal.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_frontomarginal.label 12 701 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_insular_long.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.G_insular_long.label 13 865 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/largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_pericallosal.label 71 3874 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_postcentral.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_postcentral.label 72 1922 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_precentral-Inferior-part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_precentral-Inferior-part.label 73 1921 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_precentral-Superior-part.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_precentral-Superior-part.label 74 205 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_subcentral_ant.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_subcentral_ant.label 75 283 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_subcentral_post.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_subcentral_post.label 76 220 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_suborbital.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_suborbital.label 77 1999 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_subparietal.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_subparietal.label 79 1276 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_temporal_inferior.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_temporal_inferior.label 80 7673 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_temporal_superior.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_temporal_superior.label 81 365 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_temporal_transverse.label LabelWrite: saving to /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078/rh.S_temporal_transverse.label mri_mergelabels -o /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/label/rh.cortex.label -d /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/make_cortex_label.tmp.17078 Done /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf mris_preproc --out rh.orig.avg.area.mgh --f /tmp/subjlist.17078 --target AO_fMRI_average --hemi rh --area orig --mean nsubjects = 5 tmpdir is ./tmp.mris_preproc.18803 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf Tue Dec 22 23:20:59 EST 2009 /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf --out rh.orig.avg.area.mgh --f /tmp/subjlist.17078 --target AO_fMRI_average --hemi rh --area orig --mean Linux bc01-n14.isis.unc.edu 2.6.18-128.7.1.el5 #1 SMP Wed Aug 19 04:00:49 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid tmpdir is ./tmp.mris_preproc.18803 --------------------------------------------------- #@# 1/5 20080724_N005/ Tue Dec 22 23:20:59 EST 2009 -------------- ----------------------- mri_surf2surf --hemi rh --srcsubject 20080724_N005/ --surfreg sphere.reg --sval-area orig --jac --trgsubject AO_fMRI_average --tval ./tmp.mris_preproc.18803/20080724_N005/.1.mgh --noreshape mghWrite(./tmp.mris_preproc.18803/20080724_N005/.1.mgh, -1): could not open file Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 20080724_N005/ srcval = (null) srctype = trgsubject = AO_fMRI_average trgval = ./tmp.mris_preproc.18803/20080724_N005/.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) Reading source surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/rh.sphere.reg Loading source data Reading surface file /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080724_N005//surf/rh.orig INFO: surfcluster: NOT fixing group surface area Reading target surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr: building source hash (res=16). Surf2Surf: 1st Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (124929) Reverse Loop had 20093 hits INFO: nSrcLost = 0 nTrg121 = 149389, nTrgMulti = 14453, MnTrgMultiHits = 2.39023 nSrc121 = 81283, nSrcLost = 0, nSrcMulti = 43646, MnSrcMultiHits = 2.35192 Saving target data --------------------------------------------------- #@# 2/5 20080729_N002/ Tue Dec 22 23:21:12 EST 2009 -------------- ----------------------- mri_surf2surf --hemi rh --srcsubject 20080729_N002/ --surfreg sphere.reg --sval-area orig --jac --trgsubject AO_fMRI_average --tval ./tmp.mris_preproc.18803/20080729_N002/.2.mgh --noreshape mghWrite(./tmp.mris_preproc.18803/20080729_N002/.2.mgh, -1): could not open file Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 20080729_N002/ srcval = (null) srctype = trgsubject = AO_fMRI_average trgval = ./tmp.mris_preproc.18803/20080729_N002/.2.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) Reading source surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/rh.sphere.reg Loading source data Reading surface file /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N002//surf/rh.orig INFO: surfcluster: NOT fixing group surface area Reading target surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr: building source hash (res=16). Surf2Surf: 1st Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (129533) Reverse Loop had 23171 hits INFO: nSrcLost = 0 nTrg121 = 147484, nTrgMulti = 16358, MnTrgMultiHits = 2.41649 nSrc121 = 86810, nSrcLost = 0, nSrcMulti = 42723, MnSrcMultiHits = 2.34541 Saving target data --------------------------------------------------- #@# 3/5 20080729_N004/ Tue Dec 22 23:21:25 EST 2009 -------------- ----------------------- mri_surf2surf --hemi rh --srcsubject 20080729_N004/ --surfreg sphere.reg --sval-area orig --jac --trgsubject AO_fMRI_average --tval ./tmp.mris_preproc.18803/20080729_N004/.3.mgh --noreshape mghWrite(./tmp.mris_preproc.18803/20080729_N004/.3.mgh, -1): could not open file Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 20080729_N004/ srcval = (null) srctype = trgsubject = AO_fMRI_average trgval = ./tmp.mris_preproc.18803/20080729_N004/.3.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) Reading source surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Loading source data Reading surface file /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.orig INFO: surfcluster: NOT fixing group surface area Reading target surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr: building source hash (res=16). Surf2Surf: 1st Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (133032) Reverse Loop had 24882 hits INFO: nSrcLost = 0 nTrg121 = 145322, nTrgMulti = 18520, MnTrgMultiHits = 2.34352 nSrc121 = 91533, nSrcLost = 0, nSrcMulti = 41499, MnSrcMultiHits = 2.34201 Saving target data --------------------------------------------------- #@# 4/5 20080729_N004/ Tue Dec 22 23:21:38 EST 2009 -------------- ----------------------- mri_surf2surf --hemi rh --srcsubject 20080729_N004/ --surfreg sphere.reg --sval-area orig --jac --trgsubject AO_fMRI_average --tval ./tmp.mris_preproc.18803/20080729_N004/.4.mgh --noreshape mghWrite(./tmp.mris_preproc.18803/20080729_N004/.4.mgh, -1): could not open file Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 20080729_N004/ srcval = (null) srctype = trgsubject = AO_fMRI_average trgval = ./tmp.mris_preproc.18803/20080729_N004/.4.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) Reading source surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.sphere.reg Loading source data Reading surface file /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080729_N004//surf/rh.orig INFO: surfcluster: NOT fixing group surface area Reading target surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr: building source hash (res=16). Surf2Surf: 1st Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (133032) Reverse Loop had 24882 hits INFO: nSrcLost = 0 nTrg121 = 145322, nTrgMulti = 18520, MnTrgMultiHits = 2.34352 nSrc121 = 91533, nSrcLost = 0, nSrcMulti = 41499, MnSrcMultiHits = 2.34201 Saving target data --------------------------------------------------- #@# 5/5 20080807_N003/ Tue Dec 22 23:21:51 EST 2009 -------------- ----------------------- mri_surf2surf --hemi rh --srcsubject 20080807_N003/ --surfreg sphere.reg --sval-area orig --jac --trgsubject AO_fMRI_average --tval ./tmp.mris_preproc.18803/20080807_N003/.5.mgh --noreshape mghWrite(./tmp.mris_preproc.18803/20080807_N003/.5.mgh, -1): could not open file Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 20080807_N003/ srcval = (null) srctype = trgsubject = AO_fMRI_average trgval = ./tmp.mris_preproc.18803/20080807_N003/.5.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) Reading source surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/rh.sphere.reg Loading source data Reading surface file /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/20080807_N003//surf/rh.orig INFO: surfcluster: NOT fixing group surface area Reading target surface reg /largefs/moana/AO_fMRI/FreeSurfer_analysis_valid/AO_fMRI_average/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr: building source hash (res=16). Surf2Surf: 1st Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (138842) Reverse Loop had 27271 hits INFO: nSrcLost = 0 nTrg121 = 144105, nTrgMulti = 19737, MnTrgMultiHits = 2.38172 nSrc121 = 98700, nSrcLost = 0, nSrcMulti = 40142, MnSrcMultiHits = 2.30215 Saving target data ----------------------- mri_concat ./tmp.mris_preproc.18803/20080724_N005/.1.mgh ./tmp.mris_preproc.18803/20080729_N002/.2.mgh ./tmp.mris_preproc.18803/20080729_N004/.3.mgh ./tmp.mris_preproc.18803/20080729_N004/.4.mgh ./tmp.mris_preproc.18803/20080807_N003/.5.mgh --o rh.orig.avg.area.mgh --mean mghRead(./tmp.mris_preproc.18803/20080724_N005/.1.mgh, -1): could not open file ninputs = 5 Checking inputs ERROR: reading ./tmp.mris_preproc.18803/20080724_N005/.1.mgh

1 0

Do I have to use two MPRAGEs to run recon-all?
by liyari5018 23 Dec '09

23 Dec '09

Hi all, Merry Cristmas!!! I have a question about recon-all: Do I have to use two MPRAGEs to run recon-all? ThX! LJ

2 1

Getting an Error at Watershed
by Alen Zamanyan 23 Dec '09

23 Dec '09

FreeSurfer Support: I am trying to execute MRI_Watershed and receive the following error: ******************************************* *********************************************** *********************************************** White matter intensity 0 is lower than CSF intensity 17. Please examine input images. Will terminate ... *********************************************** *********************************************** *********************************************** ********************************************************** MRIstripSkull failed. ************************************************************ What could be wrong with the input volume? How can I fix this? Any ideas? Thanks, Alen

2 1

Announcement: 2010 FSL & FreeSurfer course in Heidelberg, Germany
by Bruce Fischl 23 Dec '09

23 Dec '09

We are pleased to announce the 2010 FSL & FreeSurfer course in Heidelberg, Germany. It will run immediately before the Human Brain Mapping conference, which will be in Barcelona - a 2-hour flight from the Heidelberg area. The course is an official satellite meeting of the HBM conference. The course lasts 5 days, from May 31 to June 4. Numbers of attendees are strictly limited and are available on a first- come-first-served basis. For full information and to register for the course, please go to: http://www.fmrib.ox.ac.uk/fslcourse/heidelberg2010.html Regards, course organisers.

1 0

make_average_subject error
by Estephan Moana 22 Dec '09

22 Dec '09

1 0

Re: [Freesurfer] recon-all problem
by Gabriel Go.Es. 22 Dec '09

22 Dec '09

Dear Bruce and FS experts I'm sending attached 2 images, 1) one with the original subject, without any transformation (just from NIfTY format to mgz format), and 2) the T1.mgz created during the recon-all step, note that the original image has the background with a higher intensity, could be the background the problem to the recon-all? is there any way to put the background to zero? Best Gabriel > Date: Tue, 22 Dec 2009 10:51:16 -0500 > From: fischl(a)nmr.mgh.harvard.edu > To: gabriellbk(a)hotmail.com > Subject: RE: [Freesurfer] recon-all problem > > Hi Gabriel, > > can you post this type of question to the list so others can answer? Send > along a snapshot of the T1.mgz also so we can take a look > Bruce > > > > On Tue, 22 Dec 2009, Gabriel Go.Es. wrote: > > > > > Thanks Bruce > > > > > > > > I have some more doubts, when you say the "talairach" what are you exacly refering to?, I've checked all the txt's named talairach, and where they say intensity is equal to 1; about the T1 mgz, it apperas almost all in withe, I guess that could be the main problem, looks like the intensity its bad, I've also checked the nu.mgz, orig.mgz and rawavg.mgz, and all of them look so withe, but the rawavg.mgz which not so withe as the others but withe too. I guess the intensity from my original image is not good, how can i fix it to make the recon-all? > > > > > > > > Regards > > > > Gabriel > > > > > > > > > > > > > > > >> Date: Tue, 22 Dec 2009 09:25:46 -0500 > >> From: fischl(a)nmr.mgh.harvard.edu > >> To: gabriellbk(a)hotmail.com > >> CC: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] recon-all problem > >> > >> check the talairach and the intensity normalization (T1.mgz) to make sure > >> they both succeeded. One or the other may need to be corrected. > >> > >> cheers, > >> Bruce > >> On Tue, 22 Dec > >> 2009, Gabriel Go.Es. wrote: > >> > >>> > >>> > >>> > >>> > >>> > >>> Dear Fs experts > >>> > >>> > >>> > >>> I'm trying to run a recon-all on one subject but FS gives me the following error message: > >>> > >>> > >>> #@# Skull Stripping Mon Dec 21 17:25:55 CET 2009 > >>> Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux > >>> > >>> recon-all exited with ERRORS at Mon Dec 21 18:11:04 CET 2009 > >>> > >>> > >>> I take a look in the log trying to fing a solution and say: > >>> > >>> > >>> > >>> ****************TEMPLATE DEFORMATION**************** > >>> > >>> second estimation of the COG coord: x=127,y=128, z=127, r=9985 iterations > >>> GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 20574 > >>> RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 99 > >>> LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 126 > >>> RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 936 > >>> LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 576 > >>> OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 18837 > >>> mri_watershed Error: > >>> GLOBAL region of the brain empty ! > >>> Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux > >>> > >>> recon-all exited with ERRORS at Mon Dec 21 18:11:04 CET 2009 > >>> > >>> > >>> > >>> > >>> what can I do to keep with the recon-all, could be something wrong in the image? > >>> > >>> > >>> > >>> Best > >>> > >>> Gabriel > >>> > >>> _________________________________________________________________ > >>> Sólo hay un loro experto en Windows 7 en todo el mundo. Y vive en Sietes ¡Cónocelo! > >>> http://www.sietesunpueblodeexpertos.com/ > > > > _________________________________________________________________ > > Date una vuelta por Sietes y conoce el pueblo de los expertos en Windows 7 > > http://www.sietesunpueblodeexpertos.com/ _________________________________________________________________ Sólo hay un loro experto en Windows 7 en todo el mundo. Y vive en Sietes ¡Cónocelo! http://www.sietesunpueblodeexpertos.com/

2 1

FSL-FS results integration
by Estephan Moana 22 Dec '09

22 Dec '09

Hello Freesurfer people, I am following the FSL-Fressurfer tutorial from the June course to look at my data on both applications. I successfully was able to register my FEAT output (non-smoothed) to the FS anatomical. My questions are for the following steps: 1. Is there a difference between resampling individual run COPE's to a common surface instead of resampling subject-level GFEAT COPE's (in native space)? If they are equivalent the second option seems to be less cumbersome when typing the mris_preproc command - is this a correct conclusion? 2. When I display individual functional runs or GFEAT results over the subject's surface, I am basically looking at FEAT/GFEAT results, correct? So when I run a surface_based group analysis using mri_glmfit how similar/different are these results from those of a group-level FEAT analysis, assuming that I used a simple one-sample group mean and fixed-effects for both analyzes? Thank you. Estephan

2 1

Averaging Multiple Scans
by Srihasam, Krishna 22 Dec '09

22 Dec '09

Hi, I have over 100 functional scans which I got from same subject over 6 different sessions. I am trying to average them and I am getting a "OUT OF MEMORY" error in "selxavg-sess" command. Is there a workaround for this problem? BTW, my machine has around 29GB of RAM. Regards, Krishna

2 1

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