Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Parcellation data order
by Neel Kishan 24 Jul '06

24 Jul '06

Hi List, Thanks for providing the mris_ca_label program and the two papers from 2004 and 2006. I'm using AFNI's FSread_annot to read the aparc.annot and aparc.a2005s.annot files into SUMA. The ROIs are imported numbered 0 to 34 for the aparc.annot files and 0 to 81 for the aparc.a2005s.annot files. I can see that the aparc.annot files correspond to the 2006 Desikan et al. paper, but I'm not sure how they were ordered in the annot file. I'm also wondering how the aparc.a2005s.annot files identified and ordered the ROIs. Thanks for your help, Neel Kishan

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generic dicom converting
by Doug Greve 24 Jul '06

24 Jul '06

I've just modified the way the DEV version of mri_convert reads in generic (ie, non-siemens) dicom files. This change makes it so that it can convert multi-frame GE (and possibly other) dicom files. Thanks to Adam Thomas at NIH for supplying the GE data. I've also fixed a slight bug in the way the coordinates in the non-siemens dicoms were read (they were off by 0.5 voxel). I suspect that no one will notice this change unless you do a "diff" between the same dicom converted with the different versions. If you want to use the old dicom reader, run mri_convert with -dicomread0. Please let me know if you have any questions or run into any problems. Also let me know if you have some data you'd like me to test it out on. I have not tested it out on diffusion data yet, for exmaple. doug

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glutInit-Bug?
by Thomas Stephan 24 Jul '06

24 Jul '06

Dear List, when I press the button to display the colorbar in tksurfer I receive the following error message, followed by a crash: freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glutInit'. There has been recent discussion about a 'glutinit-bug', but I could not find the solution for the problem in the archives. By the way: How can I find out which version of freesurfer I use? tksurfer tells me I use version stable 3. Best regards Thomas Stephan -- ====================================================================== Dr. Thomas Stephan Email: tstephan(a)nefo.med.uni-muenchen.de Klinikum Grosshadern Neurologisches Forschungshaus Marchioninistr. 23 Fon: +49 089 / 7095-4819 81377 Muenchen Fax: +49 089 / 7095-4801 ======================================================================

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FW: help install freesurfer
by Fleisher, Adam 23 Jul '06

23 Jul '06

I am trying to install Freesurfer on RedHat Linux EL3 x86_64. I am using a csh shell and the setup seems to work fine. But, when I test tkmedit, it gives me an error: "tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory" I have seen threads that say I need to locate libglut and create a symbolic link from libglut.so.3 to my current version. Where is libglut located and how do I create a link? Anyone have this problem with explicit fix instructions? Thanks, Adam

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recon-all malloc error
by Rutvik Desai 21 Jul '06

21 Jul '06

recon-all exited with the following error. Running on a Powermac G5 with 1G ram. Any ideas? thanks, Rutvik --------------------------------------------- Fix Topology rh Thu Jul 20 13:29:52 CDT 2006 /usr/local/freesurfer/subjects/2628/scripts mris_fix_topology 2628 rh reading input surface /usr/local/freesurfer/subjects/2628/surf/rh.qsphere... before topology correction, eno=-510 (nv=191807, nf=384696, ne=577013, g=256) using quasi-homeomorphic spherical map to tessellate cortical surface... mris_fix_topology(124) malloc: *** vm_allocate(size=2075615232) failed (error code=3) mris_fix_topology(124) malloc: *** error: can't allocate region mris_fix_topology(124) malloc: *** set a breakpoint in szone_error to debug could not allocate 16108 edges for retessellation Cannot allocate memory reading T1 volume from T1... reading wm segmentation from wm... 136542 ambiguous faces found in tessellation 246 of 4410 overlapping edges discarded 1 of 299 overlapping edges discarded 175 of 1655 overlapping edges discarded retessellating defect 3 with 4269 vertices (convex hull=26247). 661414 of 8448632 overlapping edges discarded 7 of 59 overlapping edges discarded 0 of 45 overlapping edges discarded retessellating defect 6 with 16108 vertices (convex hull=7747). ERROR: mris_fix_topology exited with non-zero status

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label coordinates
by Doug Greve 21 Jul '06

21 Jul '06

Kevin has changed the way freesurfer writes labels. Previously, the coordinates were from the orig surface. From now on (in the development distribution) they will correspond to the white surface. As Kevin points out, the surface from which the coordinates were derived will be in the first line of the label file to help us keep track of the change. doug -------- Original Message -------- Subject: [Fsdev] tksurfer labels now written in white space Date: Fri, 21 Jul 2006 10:48:10 -0400 From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> To: fsdev(a)nmr.mgh.harvard.edu I changed label.c and label.h to add a text field. The LabelToXXX functions write a note to that field, "coords=XXX". LabelWrite now writes this field in the comment line of the label. I replaced all calls to LabelToOriginal in tksurfer with calls to LabelToWhite. -- Kevin Teich _______________________________________________ Fsdev mailing list Fsdev(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fsdev -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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FLASH atlas
by Derin Cobia 21 Jul '06

21 Jul '06

Hello, I read in the archive that you were planning on releasing two new atlases (for MP-RAGE and FLASH) last year. Were those (or even newer ones) distributed? I have some FLASH sequences I want to run. Thanks! -Derin

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source of thickness information for mris_preproc
by Lars M. Rimol 21 Jul '06

21 Jul '06

Hi, When one runs mris_preproc with e.g. -meas thickness, does it get the thickness information from the files in the stats directory within each subject's directory - or from the ?h.thickness files under the surf directories? Thank you! -- yours, LMR

3 2

freesurfer movies
by Thomas Stephan 20 Jul '06

20 Jul '06

Dear List, I used tksurfers 'make frame' button to save frames to a movie. What type of movie file is generated by this function, and which viewer or converter could I use to see or convert it? Best regards Thomas -- ====================================================================== Dr. Thomas Stephan Email: tstephan(a)nefo.med.uni-muenchen.de Klinikum Grosshadern Neurologisches Forschungshaus Marchioninistr. 23 Fon: +49 089 / 7095-4819 81377 Muenchen Fax: +49 089 / 7095-4801 ======================================================================

2 1

recon-all error
by sbasho＠nmr.mgh.harvard.edu 20 Jul '06

20 Jul '06

Hello, I received an error when running recon-all. It seems to have run into a problem during the 'Remove Neck' and 'SkullLTA' steps. I have included the output below of the last two steps before the error occured. Thank you. -Surina #@# Remove Neck Wed Jul 19 15:26:17 EDT 2006 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... mghWrite(nu_noneck.mgz, -1): could not open file gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11405488 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 23 minutes and 41 seconds. #-------------------------------------- #@# SkullLTA Wed Jul 19 15:50:02 EDT 2006 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/stable/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization = 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /autofs/space/tango_003/users/recon_modygp/surina/mody096/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/autofs/space/tango_003/users/recon_modygp/surina/mody096/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz. Linux whump 2.6.9-34.ELsmp #1 SMP Wed Mar 8 00:27:03 CST 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Jul 19 15:50:30 EDT 2006

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