Re: [Freesurfer] Stats and viewing parcellation problem

-- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego San Diego State University/University of California, San Diego Joint Doctoral Program in Clinical Psychology VA San Diego Healthcare System Mailcode 151C 3350 La Jolla Village Drive San Diego, CA 92161 Office: 858-552-8585 x6109 > From: Yasunari Tosa tosa@nmr.mgh.harvard.edu > Date: Tue, 07 Dec 2004 13:14:14 -0500 > To: Xander Meadow xmeadow@uchicago.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Stats and viewing parcellation problem > > This is just a bug fix for tksurfer, reading annotation file. > Nothing related to afni script. > > Tosa > > Xander Meadow wrote: > >> Just a quick question, will this update be incorporated if I use the >> UPDATER script from the afni website? I don't necessarily mean right >> now, but upon the next upgrade. Thanks. >> >> >> >>> Xander >>> >>> >> >> On Tue, 2004-12-07 at 11:44, Yasunari Tosa wrote: >> >> >>> Fixed MacOSX version of tksurfer is available on our ftp page. >>> >>> $ ftp surfer.nmr.mgh.harvard.edu >>>> username: anonymous >>>> passwd: (your email address) >>>> cd /transfer/outgoing/birn/tosa/Update/Mac >>>> bin >>>> get tksurfer >>> >>> I verified this works under Powerbook G4 running Panther. >>> Should work for G5 (not compatible with G3). If you have problems, let >>> me know. >>> >>> Tosa >>> >>> Brian Schweinsburg, Ph.D. wrote: >>> >>> >>> >>>> Sounds good. Thanks. >>>> Brian >>>> >>>> >>>> >>>> >>>> >>>> >>>>> From: Bruce Fischl fischl@nmr.mgh.harvard.edu >>>>> Date: Tue, 7 Dec 2004 11:50:50 -0500 (EST) >>>>> To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu >>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>>> Subject: Re: [Freesurfer] Stats and viewing parcellation problem >>>>> >>>>> Hi Brian, >>>>> >>>>> this is a bug that Tosa has fixed. He has a new Mac version of tksurfer >>>>> that he'll send you shortly. >>>>> >>>>> cheers, >>>>> Bruce >>>>> >>>>> >>>>> On Mon, 6 Dec 2004, Brian Schweinsburg, Ph.D. wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> Hi All, >>>>>> >>>>>> I am having problems computing stats using the parcellation file. In >>>>>> addition, when I try to display the parcellation results in tksurfer >>>>>> (File >>>>>> -> Label -> Import Annotation -> rh.aparc.annot), which were completed >>>>>> without an error message using parcellate_subject-rh, I get an error >>>>>> message. I am not sure how to procede. Any hints? >>>>>> >>>>>> In both error logs, there is a reference to an older location of the >>>>>> Simple_surface_labels2002.txt file, which never existed on my machine. Is >>>>>> that related to the problem? >>>>>> >>>>>> My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218. >>>>>> >>>>>> I appreciate any assistance. >>>>>> Brian >>>>>> >>>>>> >>>>>> >>>>>> ####### >>>>>> mris_anatomical_stats error message >>>>>> ####### >>>>>> mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot >>>>>> SC002 >>>>>> rh >>>>>> computing statistics for each annotation in >>>>>> /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.a >>>>>> nno >>>>>> t. >>>>>> reading volume >>>>>> /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... >>>>>> reading input surface >>>>>> /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... >>>>>> Computing inter-vertex distance >>>>>> >>>>>> computing second fundamental form...reading colortable from annotation >>>>>> file... >>>>>> colortable with 85 entries read (originally >>>>>> /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) >>>>>> reading colortable from annotation file... >>>>>> *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 >>>>>> CTABreadFrom: could not allocate -1073747536 bin table >>>>>> Cannot allocate memory >>>>>> Bus error >>>>>> >>>>>> ####### >>>>>> Tksurfer error message >>>>>> ####### >>>>>> reading colortable from annotation file... >>>>>> colortable with 85 entries read (originally >>>>>> /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) >>>>>> *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 >>>>>> CTABreadFrom: could not allocate -1073756992 bin table >>>>>> Cannot allocate memory >>>>>> >>>>>> Command Finished >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> >>>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > -- > Yasunari Tosa, Ph.D. Email: tosa@nmr.mgh.harvard.edu > NMR Ctr, Mass. General Hospital TEL: 617-726-4050 > Building 149, 13th Street > Charlestown, MA 02129 > USA > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer