Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

output from single subject sphere morph to atlas
by Lars M. Rimol 27 Jul '06

27 Jul '06

Hi, Is the determinant of the Jacobian matrix for the sphere morph to atlas space saved vertex by vertex? If so, where is it saved? -- yours, LMR

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recon-all exited with ERRORS
by Chacko Cherian 26 Jul '06

26 Jul '06

Hello all, I was running recon-all for one of my images and this happened to be the error that i got.what is libstdc++?? Could someone please clarify, Thanks in advance Chacko. "mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Wed Jul 26 13:09:41 MST 2006" __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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display SPM group results
by Thomas Stephan 26 Jul '06

26 Jul '06

Dear FSL list, I would like to use freesurfer to render fMRI results obtained by SPM group analysis onto inflated surfaces of the template brain. I succeeded to do so by inflating the template provided with SPM and using tkregister2 with the functional data. Are there any recommendations for this procedure with regard to the template to use, or should I use the fsaverage surfaces provided with freesurfer? 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 ======================================================================

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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

3 2

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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