Freesurfer March 2008

freesurfer@nmr.mgh.harvard.edu

55 participants
81 discussions

help for mri_surfcluster command(resubmit).
by Zhen Zonglei 05 Mar '08

05 Mar '08

Hi,all: I have some questions related to the command of mri_surfcluster (and mri_volcluster). The help of this command says cwsig option can give the cluster-wise sig-map, but vwsig option will give vertex-wise sig-map. What is the exact meaning of these options? Does every voxel in one specific cluster have a common p value in cwsig-map (refer to significance of the cluster)? Does every voxel in one specific cluster have different p values in vwsig-map (refer to significance of the voxel)? Should the p value of one specific voxel in vwsig-map equal to its p value in the original sig-map (non-corrected)? I want to display the corrected cluster map, but hope every voxel in a cluster have a p value of itself. how to implement this function? Thanks in advance. Zonglei Zhen

1 0

optseq2 generation time
by Shannon Tubridy 05 Mar '08

05 Mar '08

Dear List - I have a question about how long I should expect it takes my computer to generate optseq2 sequences. A colleague advised that I should expect it to take a couple hours to generate sequences. I've just produced 20 sequences (nsearch = 10000; see below for full command line specs) on a powerpc Mac (dual 1.8 GHz) and it took less than a minute. Everything appears reasonable in the generated sequences (although there are five columns in my par files, including a mysterious fourth column with 1 in every entry in every par file), but I'm concerned that something went wrong because it went so fast. Any advice is appreciated. --------------------------------- optseq2 --ntp 270 / --tr 2 / --psdwin 0 20 / --ev event1 4 45 / --ev event2 4 30 / --ev event3 4 30 / --nkeep 20 / --o Sub / --nsearch 10000 --------------------------------- Shannon Tubridy NYU Dept of Psychology 6 Washington Place - 8th floor New York, NY 10003

2 1

FW: qdec segmentation faults
by Nicolas Cherbuin 05 Mar '08

05 Mar '08

Hi, I am using FS 4.01. I have processed 400 scans with autorecon-all. I am trying to analyse ~350 of them in qdec. I have done the preprocessing (recon-all -qcache -measure thickness) and prepared the required files (attached). I can start qdec and conduct an analysis. I can also visualise some results but invariably after moving between the contrasts a seg fault occurs (logs attached, I was going to attach 2 but one of them was 12MB in size, does this sound like a normal output length?). I have a dual quad core Xeon 5355 with 8 Gig of RAM and plenty of disk space. I don't think it makes any difference but just in case... I computed my own average. Make_average_surface went ok but make_average_volume was killed because it required too much resources. I figured I did not require the volume for the qdec analysis so I used my average (older people) for -qcache smoothing. However, when I first tried to visualise the results qdec did not like the fact that there was no curvature information (I was going to attach a log file but it was 6MB in size) in my average subject so I linked to fsaverage. Any help is welcome. Cheers Nic

2 2

Memory Problem when running mris_volmask
by gonzalj＠purdue.edu 05 Mar '08

05 Mar '08

Hello, When I run the command "mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1" I get the following error: ERROR: opening pipe gzip -f -c > /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno = 12 Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, -1): could not open file I had this error on a previous step and managed to solve it by means of using directories with COR files instead of a single mgz file for input and output. I do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not run into a memory problem? Also, any other ideas? Thanks a lot, Javier.

2 6

qdec missing data
by Hoppmann, Fee 05 Mar '08

05 Mar '08

Hi all, can you tell me if there is a possibility to run qdec analysis with missing data? When I just leave it out I get an "GetContiniousFactor"-error. But I'd really like to include those variables. Thank you! Fee

3 2

Some questions related to f mri_surfcluster.
by Zhen Zonglei 05 Mar '08

05 Mar '08

Hi，all: I have some questions related to the command of mri_surfcluster (and mri_volcluster). The help of this command says cwsig option can give the cluster-wise sig-map, but vwsig option will give vertex-wise sig-map. What is the exact meaning of these options? Does every voxel in one specific cluster have a common p value in cwsig-map (refer to significance of the cluster)? Does every voxel in one specific cluster have different p values in vwsig-map (refer to significance of the voxel)? Should the p value of one specific voxel in vwsig-map equal to its p value in the original sig-map (non-corrected)? I want to display the corrected cluster map, but hope every voxel in a cluster have a p value of itself. how to implement this function? Thanks in advance. Zonglei Zhen

1 0

Cortical thickness map
by Juergen Haenggi 05 Mar '08

05 Mar '08

Dear FS experts I overlaid the thickness file of a single subject (see attachment). When I showed the colour bar there are no values presented and the colour bar appears in blue and red (as in F- or t-contrast) with grey in between. Why there are grey islands and how to present the thickness values in mm that corresponds to the colour of colour bar? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

1 0

mris_thickness_diff ERROR
by Scott Beeman 04 Mar '08

04 Mar '08

Hello, I am trying to use Xiao Han's ThicknessRepeatability methods for a longitudinal study. I have successfully completed step one, which is rigid registration of the pre and post scans, but I am having problems with step 2. This step uses the mris_thickness_diff function to compute the thickness difference map. I use the following command, as suggested by Xiao Han: mris_thickness_diff -xform $SUBJECTS_DIR/1001/mri/transforms/1001_to_1001a.lta \ -src_type curv \ -out $SUBJECTS_DIR/1001/surf/lh.thickness_diff.mgh \ -nsmooth 0 \ -abs -S 1001 \ -L $SUBJECTS_DIR/1001/surf/lh_thickness_diff.log \ $SUBJECTS_DIR/1001/surf/lh.white \ $SUBJECTS_DIR/1001/surf/lh.thickness \ $SUBJECTS_DIR/1001a/surf/lh.white \ $SUBJECTS_DIR/1001a/surf/lh.thickness The function successfully reads the surfaces, but if fails when trying to apply the LTA xform to align surface 1 to surface 2. The terminal states: INFO:try to get src info from transform. ERROR: ComputeDifferenceNew: MHTfindClosestVewrtexNo returned nnindex=-1, which is invalid I have experienced this error for multiple subjects and have been unable to get past it. I am unsure of what the nnindex is and why it is -1. Any help on this issue would be greatly appreciated. Thanks. -Scott Beeman

2 1

Odd tkmedit behavior
by Dan Dillon 04 Mar '08

04 Mar '08

Dear FreeSurfers, I have overlaid group data on the fsaverage brain, and find that when I type Talairach coordinates into tkmedit (e.g., 9.90 -36.64 -14.15), the cursor jumps to a nearby but different location (e.g., 9.8 -36.1 -10.1). Any ideas what could be causing this trouble? Thanks! Dan Dillon

3 8

question about generating wmparc.stats
by Teddy Youn 04 Mar '08

04 Mar '08

Hi again, I had a quick question about generating wmparc.stats. I have tried to run recon3 with the -wmparc flag and have encountered an error where ?h.smoothwm is not being read even though my /surf folder has the files. Below is the output of what occurs in my xterm. We have v4.0.2 of FS on Leopard 10.5.2. Thanks in advance, -t ============================================================================== recon-all -autorecon -wmparc -no-isrunning -subjid St14-Initial INFO: SUBJECTS_DIR is /Volumes/ZetaData/Teddysfolder/CorrectedBrainsSiemens/TBISt14 Actual FREESURFER_HOME /Applications/freesurfer -rwxrwxrwx 1 teresa teresa 2712975 Mar 3 17:41 /Volumes/ZetaData/Teddysfolder/CorrectedBrainsSiemens/TBI/St14/St14-Initial/scripts/recon-all.log Darwin 0-1d-4f-48-96-f4.dyn.utdallas.edu 9.2.0 Darwin Kernel Version 9.2.0: Tue Feb 5 16:13:22 PST 2008; root:xnu-1228.3.13~1/RELEASE_I386 i386 #-------------------------------------------- #@# Sphere lh Mon Mar 3 17:43:27 CST 2008 /Volumes/ZetaData/Teddysfolder/CorrectedBrainsSiemens/TBI/St14/St14-Initial/scripts \n mris_sphere ../surf/lh.inflated ../surf/lh.sphere \n $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ $Id: mrisurf.c,v 1.557.2.5 2007/12/10 20:20:29 nicks Exp $ reading original vertex positions... MRISreadVertexPositions(../surf/lh.smoothwm): surfaces differ. Main: 194252 ver s 390408 faces, smoothwm: 188404 verts 378044 faces No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory Darwin 0-1d-4f-48-96-f4.dyn.utdallas.edu 9.2.0 Darwin Kernel Version 9.2.0: Tue Feb 5 16:13:22 PST 2008; root:xnu-1228.3.13~1/RELEASE_I386 i386 recon-all exited with ERRORS at Mon Mar 3 17:43:30 CST 2008 Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

2 1

← Newer
1
2
3
4
5
6
7
8
9
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer March 2008