Freesurfer October 2007

freesurfer@nmr.mgh.harvard.edu

55 participants
79 discussions

QA tools--Permission denied??
by Pratap Kunwar 09 Oct '07

09 Oct '07

hi all I tried to use QA tools on the wiki (writen by jpacheco) at https://surfer.nmr.mgh.harvard.edu/fswiki/QATools?action=highlight&value=qa…. I got the following error saying permission denied. I could not even copy the QATOOLS to my folder. thanks pratap [galen:S4_HR_LR18_recon] (nmr-std-env) setenv QA_SCRIPTS /space/tensor/17/users/jpacheco/QAtools [galen:S4_HR_LR18_recon] (nmr-std-env) $QA_SCRIPTS/data_checker/recon_checker -nocheckasegoutliers -s rfa1410 -o QAsnap.html /space/tensor/17/users/jpacheco/QAtools/data_checker/recon_checker: Permission denied. -------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071006 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18_recon/ PWD: /space/galen/2/users/carl/S4_HR_LR18/S4_HR_LR18_recon

2 1

Displaying cortical thickness
by Martin Kavec 08 Oct '07

08 Oct '07

Hi, I would really appreciate a help (steps or a link to description) on how to display cortical thinning on an inflated surface. I ran a subject through recon-all -autorecon3 and now I would basically want to see, where (s)he has abnormal thickness of the cortex. Thanks a lot in advance, Martin

3 2

how to apply transformation into other dataset?
by lan lin 08 Oct '07

08 Oct '07

I have some functional data coregistered to MRI, is it possible to apply linear and nonlinear transformation that we got at MRI recon-all to those functional data?

2 1

preproc-sess failure on Mac
by Shigeaki Nishina 08 Oct '07

08 Oct '07

I'm trying to use freesurfer/fsfast on Mac Pro and found preproc-sess fails in mcparams2etreg. The problem seems actually in Mac version of MATLAB, which does not terminate properly when it finishes processing the piped code without an explicit 'exit' at the end of it (I asked Mathworks and confirmed this is a bug existing in all MATLAB versions for Mac OS X). Because the MATLAB process does not quit, mcparams2etreg can not continue processing the rest. A workaround for this problem is to put a wrapper script that calls matlab after adding 'exit' at the end of the piped code, with the name of 'matlab' in the shell path. Is this a known issue? -- Shigeaki Nishina

1 0

Question on fs-fast
by lan lin 08 Oct '07

08 Oct '07

I'm trying to use fs-fast to analysis the PET data, but found that the first level analysis is specially designed for fmri. Is there any way to use fs-fast to analysis the PET data?

1 0

selxavg-sess error
by raij＠nmr.mgh.harvard.edu 08 Oct '07

08 Oct '07

Hi Doug, selxavg-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf sessid7 -df sesspar -noomnibus exits with the error: ... Saving offset to group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h-offset_000.bfloat Slice 1, 77.2438 -------------- ??? Error using ==> minus Matrix dimensions must agree. Error in ==> fast_selxavg at 439 extreg = extreg - repmat(mean(extreg), [ntrs 1]); >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): selxavg failed I suspect this may have to do that, for each of the seven subjects, there are three runs with an unequal number of TRs. Oddly enough, the same analysis worked in March 07. Is there a way to make this analysis work again? I am only interested in BOLD% signal change (FIR waveforms) so comparing runs with different numbers of TRs should be legal. What I would like to do is to calculate a single fixed effects group analysis where each of the three run types is output as its own category (the paradigm files are coded to allow that). Only runs that have the same number of TRs are collapsed across subjects. (Running three separate analyses, one for each run type, would not help, as we need the output to be in a single block with multiple categories, just as in our earlier analysis) Or maybe the error has to do with something else... my matlab setup.m should be fine to my knowledge. machine: cuzco nmr-dev-env (same error with the standard edition) cd /space/cuzco/14/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage Thanks!!! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

2 2

TkmEdit message
by Anil Roy 05 Oct '07

05 Oct '07

Hi, When I run tkmedit, I receive the following message. It doesn't seem to affect the functionality. Could you explain why this message shows up. Xlib: extension "XFree86-DRI" missing on display ":0.0". Thanks, Anil.

2 2

multiple surface overlays
by Cameron Ellis 05 Oct '07

05 Oct '07

Hi all, Sourcing stable3, using tksurfer, does anyone know how to load more than one overlay at a time from the command line? (something like: tksurfer <subject> <hemi> <surface> -overlay1 ??? -overlay2 ??? overlay3 ???) Does this require scripting w/ tksurfer? Cameron

3 2

help on installation under VMWARE + suse 10.2
by Xue,Gui 05 Oct '07

05 Oct '07

hi-I am trying to install freesurfer my computer with the following settings: Operating system: Win XP Open Suse10.2 running under vmware workstation 6.0. Display card: NVIDIA Quadro FX 3400/4400. The problem I have is that the tksurfer doesn't work well, like what's described on the wiki, only small part of the surfer was shown. I updated the display card driver, but it didn't fix the problem. I wonder if anyone has successfully configure the system to make it work. Thanks a lot! gui

2 1

previous FS versions
by Michael Harms 05 Oct '07

05 Oct '07

Hello, Is it possible to get a version of Freesurfer other than the most current? In particular, I'm interested in getting a copy of v3.0.5 for the CentOS (RHEL 4) Linux platform. thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer October 2007