Re: [Freesurfer] mris_divide_parcellation

perfect. thanks, all of you, for your help. On May 10, 2007, at 7:55 PM, Nick Schmansky wrote: Catherine, It looks like you have a Mac. You can get mris_divide_parcellation for that here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev macppc directory is for the

[Freesurfer] mris_anatomical_stats

Hi, I'm trying to get the anatomical statistics for a new parcellation, ? h.aparc.splitcingulate.annot, I've created using mris_divide_parcellation. I've tried using mris_anatomical_stats with various argument structures (specifying output filenames, not specifiying output filenames) and

Re: [Freesurfer] mris_anatomical_stats

Hi Cate, I think you have to use the -f flag to specify an output file, otherwise it just prints to the screen. mris_anatomical_stats usage: mris_anatomical_stats [options] subject name hemi [surface name] This program measures a variety of anatomical properties valid options are: -i

Re: [Freesurfer] mris_anatomical_stats

Cate, Does the -f filename option work? try adding: -f mm103184/stats/lh.aparc.splitcingulate.stats N. On Fri, 2007-05-11 at 13:27 -0400, Catherine Hartley wrote: Hi, I'm trying to get the anatomical statistics for a new parcellation, ? h.aparc.splitcingulate.annot, I've created

[Freesurfer] bus error when loading annotation

Hi, When I attempt to load a custom annotation file (that I created using mris_divide_parcellation) within tksurfer, I get a bus error which seems to result from a problem with the colortable: % reading colortable from annotation file... CTABreadFrom: could not allocate -2 bin table Cannot

Re: [Freesurfer] mris_anatomical_stats

On May 11, 2007, at 1:38 PM, Catherine Hartley wrote: Hi Jenni, This doesn't work either: [catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -f mm103184/stats/ lh.aparc.splitcingulate.stats -a mm103184/label/ lh.aparc.splitcingulate.annot Any

[Freesurfer] recreating aparc.stats, aparc+aseg.mgz

Hi, I have parcellations that I've manually edited, and want to recompute the aparc.stats and aparc+aseg.mgz files to reflect what I've done. From the help file, I'm guessing the correct command for that is something like below, but wanted to verify: recon-all -parcstats2 -aparc2aseg -subjid

Re: [Freesurfer] mris_anatomical_stats

Cate, As wacky as this may seem, you have to put the flagged options first, then the required items, otherwise the flagged options will be blindly ignored (it took me a while to figure this out in the code). So try: mris_anatomical_stats \ -f mm103184/stats/lh.aparc.splitcingulate.stats \

Re: [Freesurfer] mris_anatomical_stats

Thanks, Nick! That seemed to be working fine until it tried to write the file, and then I got the same bus error that I emailed about before. Is there something I need to do with the color table when I create a new parcellation. [catemac:freesurfer/subjects/reruns] cate%

Re: [Freesurfer] mris_anatomical_stats

Cate, I can't seem to reproduce that bus error on our Intel Mac with plain data. Can you send me that subject in a tarball? tar cvf mm103184.tar mm103184/ gzip mm103184.tar You can upload it to me via our secure file drop: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

[Freesurfer] Editing Segmentation Results

I am new to FreeSurfer and am attempting to segment T1 images using the recon-all...autorecon2 command. The segmentation results look quite accurate, but I was wondering how to best edit the results (where there is a need). I noticed on the Wiki a possible option using I think either 3D

Re: [Freesurfer] Difficulties with segmentation follow-up

Hi Jeffrey, yes, we do have a fix and are working on getting it released. Hopefully not too long, but probably not before ISMRM and HBM. cheers, Bruce On Fri, 11 May 2007, Jeffrey Spielberg wrote: Hi, just wondering if a fix for this problem (labeling parts of acc as corpus callosum or