Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Fw: csurf failure
by Tetsuya Iidaka 09 Dec '04

09 Dec '04

Dear experts. I installed FreeSurfer (Snapshot full version) on Linux(recent version of TurboLinux) Pentium4 PC. Source SetUpFreeSurfer.csh process was successful, but when I entered "csurf" command, following error message appeared. "/home/XXX/freesurfer//bin/noarch/csurf: permission denied" .license file is in /freesurfer/ directory. Any help is very much appreciated. Tetsuya Iidaka Dept of Psychology, Nagoya University iidaka(a)info.human.nagoya-u.ac.jp

3 2

how to set the number of vertex ?
by tulu 09 Dec '04

09 Dec '04

Dear freesurfer expert, I am a new user of freesurfer. When I use mri_tessellate, how to set the number of vertex ? Thanks replay JLH

3 2

mris_anatomical_stats
by Calabrese Massimiliano 08 Dec '04

08 Dec '04

Hi everybody, Currently, we can use mris_anatomical_stats to report statistics such as thickness +/- std. dev. over the list of brain regions, as created by the parcellate_subject program. We are wondering if it is currently possible to produce similar statistics, but not just on thickness, etc., but also on data that we can supply externally. For example, we can create a file that contains a list of nodes and corresponding data values. Is it possible to have the mris_anatomical_stats program create statistics on a region-by-region basis from our supplied data? Thanks a lot for your help Massimiliano Calabrese Imaging Group NeuroImmunology Branch NIDS, NIH and Rick Reynolds SSCC/NIMH/NIH

2 1

Stats and viewing parcellation problem
by Brian Schweinsburg, Ph.D. 07 Dec '04

07 Dec '04

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.anno 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

4 7

wmfill
by Margaret Duff 06 Dec '04

06 Dec '04

Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret

3 13

Re: [Freesurfer] from volume to surface
by Joongnam Yang 03 Dec '04

03 Dec '04

Thanks, Doug, When you visually check the registration, using tkregister2 --s subjid --targ struc_fs_t1.img --mov YUNG070904_41.img --regheader --reg register.dat. two windows show up. Is there a source, or instructions, or manual, regarding what to do with the two winows? Nam.

2 1

Re: [Freesurfer] from volume to surface
by Joongnam Yang 03 Dec '04

03 Dec '04

Thanks, Doug, By any means, does the following register.dat look incorrect? subjid 3.800000 5.000000 0.150000 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 -1.525879e-05 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 round Nam.

2 1

Re: [Freesurfer] from volume to surface
by Joongnam Yang 03 Dec '04

03 Dec '04

Sorry, Doug Here is the full command and log with segmentation fault. Nam. ================== mri_vol2surf --src FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --surf occip.patch.flat --out ./thresh_zstat1-lh.w --out_type paint INFO: output format is paint srcvol = FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.img srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = occip.patch.flat hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.img ----------------------------------------------------------------- INFO: could not find FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).INFO: if not valid, please provide the information in FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 5.52912 Done loading volume Reading surface /home/nam//blobby/surf/lh.occip.patch.flat Segmentation fault (core dumped) =========================

2 1

from volume to surface
by Joongnam Yang 03 Dec '04

03 Dec '04

I have a functional volume, and a surface (occipital lobe cut, not the whole cortext) and I want to create *.w file using mri_vol2surf. mri_vol2surf gives me "segmentation fault", probably because the volume and the surface do not match. Could someone give me a clue on how to create a *.w file using mri_vol2surf when functional is whole and anatomical is only partial surface of the whole cortex? Thanks in advance. Nam.

2 1

ROIs
by aleontie＠meded-mail.ucsd.edu 01 Dec '04

01 Dec '04

Hi, > I'm trying to do something I think is pretty easy. I created some ROIs in afni(that I also have > in analyze format). I would like to overlay them onto inflated and folded surfaces > produced in freesurfer. Should I treat these as functional overlays and treat it > as functional data or is there another way? > Thanks, Oleg Leontiev

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer