Freesurfer July 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
88 discussions

Queue tasks?
by Jake Freimer 25 Jul '06

25 Jul '06

I was wondering if it is possible to queue up various subjects like if the computers were going to be left for several days to run autorecon1 and 2 on a subject, and when that finishes move on to the next subject etc. If it is not possible in freesurfer has anyone written a script that I could use to do this kind of thing? Thanks -- -Jake

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parcellate_subject error
by Darren Weber 25 Jul '06

25 Jul '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 What is this error: endorphin.16> parcellate_subject ucsf_wa could not open translation file /home/dweber/freesurfer/home/Simple_surface_labels2002.txt mris_ca_label: could not read annotation file /home/dweber/freesurfer/home/Simple_surface_labels2002.txt... No such file or directory - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFExVw6xaCYN7qs0v4RAkLUAJ9BNVQgy/oyu9I0BXu3oAdnce5kVACglRYJ F6VQxAqkmFwhRheo9pnztGc= =RANa -----END PGP SIGNATURE-----

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Re: [Freesurfer] mri_em_register args, ICV, etc
by Graham Wideman 24 Jul '06

24 Jul '06

(...and now to the list, for closure...) Jenni: Ah-ha, got it -- "hidden" in the comments :-) Thanks, Graham At 7/24/2006 02:44 PM, Jenni Pacheco wrote: >The ICV is calculated during the -segstats step with all of the other >volume measures that use the aseg. They are all found within the >aseg.stats file in the stats subdir. > >Jenni

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mri_em_register args, ICV, etc
by Graham Wideman 24 Jul '06

24 Jul '06

Folks: A couple of weeks ago, Bruce noted that: > EM Registration with Skull is for generating ICV measures ... so I just got around to investigating where the ICV measures might be getting saved. Bottom line is I don't see what file that ICV measure is getting saved into. Details: I tried to figure out which program/script does this step, and what files it produces which might capture ICV. 1. Which commands correspond to the "EM Registration with Skull" step? Clue: wiki recon-all shows this step employs the <no>skull-lta step. Looking in recon-all script, this corresponds to the DoSkullLTA variable, and that in turn leads us to mri_em_register as the pertinent command. 2. Looking at docs for mri_em_register in the wiki shows 4 arguments, only one of which is flagged. Looking at actual help output from mri_em_register shows about 50 flagged arguments, none described. 3. The pertinent bit of script looks like this: set xopts = `fsr-getxopts mri_em_register $XOptsFile`; set cmd = (mri_em_register -skull -t transforms/talairach.lta \ $xopts nu_noneck.mgz $FREESURFER_HOME/average/$GCASkull \ transforms/talairach_with_skull.lta) 4. From all this, I don't see what output file mri_em_register might be placing the ICV into. Clues? Thanks, Graham

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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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Freesurfer July 2006