[Freesurfer] error message of mris_register

Hi, We're getting an error message saying: $FREESURFERHOME/average/rh.average.curvature.filled.buckner40.tif : Not a TIFF file, bad magic number 65535 (0x). MRISPread($FREESURFERHOME/average/rh.average.curvature.filled.buckner40.tif): could not open file No such file or

Re: [Freesurfer] error message of mris_register

does the file: $FREESURFERHOME/average/rh.average.curvature.filled.buckner40.tif exist? It should be part of the installation. cheers, Bruce On Wed, 9 Jul 2008, Deniz KATIRCIOGLU wrote: Hi, We're getting an error message saying:

[Freesurfer] seg edits

Running Freesurfer v4.0.5 on RHEL5 linux system. General Question: after using the Edit Segmentation tool and saving edits by overwriting the aseg.mgz file generated during $recon-all -autorecon-all...which command should I pass to re-enter the analysis pipeline at the most appropriate spot? I

Re: [Freesurfer] deflate compression support

Thank you very much, that solved my problem. However, though I can now write .tif files, freesurfer does not seem to want to read them (when using mris_register): [Macintosh-10:/Volumes/Data/monkey_surface_data] work% mris_make_template rh sphere bu_edited monk_temp0.tif creating new

Re: [Freesurfer] error message of mris_register

I have also been having similar trouble with mris_register: [dynamic-oit-vapornet-c-124:Data/monkey_surface_data/bu_edited] work% mris_register surf/rh.sphere $SUBJECTS_DIR/monk_temp0.tif surf/ rh.sphere.reg $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ $Id: mrisurf.c,v

[Freesurfer] mgh2 stc

Hi Does anybody have a code to convert mgh format to stc? best Nima Nima Dehghani MD. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] error message of mris_register

Jan, I've put an updated mris_register here: wget ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/macintel/mris_register there may be other problem binaries, just let me know. Nick On Wed, 2008-07-09 at 11:14 -0400, Jan Kalkus wrote: I have also been having similar

[Freesurfer] percent signal change

Hello. I obtained the percent signal change using roisummary-sess. (divided the BOLD amplitude by the mean functional baseline offset to get the percent signal change.) Is there a way to get an error estimate (i.e. standard deivation) on this value? Thanks Elif

Re: [Freesurfer] error message of mris_register

Thanks a lot. It's working so far. On Jul 9, 2008, at 12:25 PM, Nick Schmansky wrote: Jan, I've put an updated mris_register here: wget ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/macintel/mris_register there may be other problem binaries, just let me know. Nick

[Freesurfer] Re: registration issue

I have 4 files: F1. anatomical image 1 F2. anatomical image 2 F3. T-map coregistered with anat img 2 F4. xfm file that coregisters anat img 2 to anat img 1. If I load all of these in scuba and apply the xfm inside scuba to the data from F2 and F3, everything aligns up nicely with the data from

[Freesurfer] major lobes of cerebellum

Is there any interest in parcellation of the cerebellum into its major regions: corpus medullare, anterior, superior-posterior, inferior-posterior regions? Any easy approaches available for testing out? Would a volume-based approach be sufficient, or would a surface-based approach be necessary?

Re: Re: Re: [Freesurfer] path error on cluster super-computer

Thanks Pedro! I've updated mri_nu_correct.mni to use a tmpdir in SUBJECTS_DIR/subjid/mri space, rather than nu_correct's default /usr/tmp, which, as Woo-Suk discovered, is not always user writable. This will appear in the next version of freesurfer. Nick On Tue, 2008-07-08 at 10:00 +0900,

Re: [Freesurfer] major lobes of cerebellum

Nikos Makris and friends have two papers on this: Journal of Cognitive Neuroscience (2003) 15:4, 584-599 Neuroimage (2005) 25, 1146-1160 Juranek, Jenifer wrote: Is there any interest in parcellation of the cerebellum into its major regions: corpus medullare, anterior, superior-posterior,

Re: [Freesurfer] major lobes of cerebellum

Hi Jenifer, We are currently working on a lobar/vermis/hemisphere labeling of the cerebellum that we intend to add to the automated segmentation procedures. Once we are done with the manual labeling, we will test the automated procedures compared to those labels. We expect that building