Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30076 discussions

Two skull strip
by Anil Roy 13 Mar '07

13 Mar '07

Hi all, Is Freesurfer going to generate all surfaces properly if I feed in a skull stripped brain to begin with starting from stage 1. In other words, is there going to be a problem if the orig.mgz is skull stripped. I checked the results after autorecon1 and the brainmask.mgz had a decent contrast. The xfm was also accurate. The brain had poor contrast(and a format that Freesurfer wouldn't recognize) so I had AFNI do the skull strip and intensity correction and then fed in that brain to recon-all. Thanks, Anil.

3 4

image rotation (answer)
by Lindsay Casmaer 13 Mar '07

13 Mar '07

The images are originally dicom that are converted to 4dfp. The 4dfp is then converted to mgz. I am unable to view the images with the tkmedit -f sessionname.dcm command I am assuming this is because we are using the 4dfp rather than dicom. The images undergo no processing in terms of flipping or rotation about the axis from dicom tot 4dfp - they are concatenated. Thanks. Lindsay On 3/12/07, Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > What is the original source of the images? If dicom, try loading the > dicom directly into tkmedit, something like: > > tkmedit -f image.dcm > > Which axis is it flipped around? > > > > Lindsay Casmaer wrote: > > > Hello, > > > > After running autorecon1 and viewing the brainmask.mgz images with > > tkmedit, the images appear rotated 180 degrees. > > > > Any suggestions on how this might be corrected would be greatly > > appreciated. > > > > The images are Seimens 3T Trio images that were converted without > > errors to the mgz format. > > > > Thanks, > > Lindsay > > > > Lindsay J. Casmaer > > Washington University in St. Louis > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >

2 1

2007 FSL & FreeSurfer Course: 3-7 September, Cardiff, Wales (fwd)
by Bruce Fischl 12 Mar '07

12 Mar '07

---------- Forwarded message ---------- Date: Tue, 13 Mar 2007 00:15:31 +0000 From: Steve Smith <steve(a)FMRIB.OX.AC.UK> Reply-To: FSL - FMRIB's Software Library <FSL(a)JISCMAIL.AC.UK> To: FSL(a)JISCMAIL.AC.UK Subject: [FSL] 2007 FSL & FreeSurfer Course: 3-7 September, Cardiff, Wales We are pleased to announce the 2007 FSL & FreeSurfer course at the School of Psychology in Cardiff University, Wales. The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with at most two attendees per computer. By the end of the course, attendees should be able to fully analyse their own FMRI and MRI data sets. For full details and registration information, see http://www.fmrib.ox.ac.uk/fslcourse/cardiff.html Regards, Course Team.

1 0

Images rotated
by Lindsay Casmaer 12 Mar '07

12 Mar '07

Hello, After running autorecon1 and viewing the brainmask.mgz images with tkmedit, the images appear rotated 180 degrees. Any suggestions on how this might be corrected would be greatly appreciated. The images are Seimens 3T Trio images that were converted without errors to the mgz format. Thanks, Lindsay Lindsay J. Casmaer Washington University in St. Louis

2 1

mris_convert
by Emily Cooper 09 Mar '07

09 Mar '07

Hi, I have a question about using mris_convert to convert .asc to .mgh. I have a .mgh file I made with mri_vol2surf (target subject as fsaverage). I convert it to .asc using this command: mris_convert -c 010.onerun.space.intval.lh.fsave.mgh /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt.asc then I try to convert it from .asc to .mgh using this command: mris_convert -c lh.010mg2txt.asc /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt2mg.mgh but when I try to load the new .mgh (lh.010mg2txt2mg.mgh) in tksurfer as an overlay: tksurfer fsaverage lh inflated & I get this error: % Loading tal xfm file /home/ecooper/subjects/fsaverage/surf/../mri/transforms/talairach.xfm MRIalloc: could not allocate 443 slices Cannot allocate memory >From the documentation of mris_convert, it seems that lh.010mg2txt2mg.mgh should be identical to the original .mgh (010.onerun.space.intval.lh.fsave.mgh). Is mris_convert unable to convert .asc to .mgh? Or is there something wrong with my commands? Thanks for your time! Emily

1 0

mri_vol2surf - analyze format error
by Johannes Klackl 09 Mar '07

09 Mar '07

Dear all, I have a problem using mri_vol2surf. My goal ist to map a functional file (Analyze format) to the surface of a specific subject and to have the registered functional image saved into Analyze format again. My command is: mri_vol2surf --src ./con_v04 --src_type analyze --trgsubject v04--srcreg register_v04.dat --hemi lh --projfrac 0.5--o ./con_v04_lh --out_type analyze. The registration file was created by spmregister by mapping the same file to the surf/orig of the subject. However, when I do this, I get the following error: ANALYZE FORMAT ERROR: ncols 73886 in volume exceeds 32768. I already tried to use the --noreshape flag, but the problem persists. Could anyone give me a hint about what I'm doing wrong? Johannes Klackl, University of Salzburg

2 1

exporting surfaces
by abel cruz vadell 09 Mar '07

09 Mar '07

Hi everyone When FreeSurfer construct the surface from the volume, does it maintain it original orientation or FreeSurfer makes internally any reorientation when normalizes the volume with Talairach? My goal is export the inflated surfaces to fusion them with another information outside the FreeSurfer and I need to know wich will be the orientation of the resulted surfaces and if I can change that orientation. Could I export both hemispheres in only one file and not splitted in two files (rigth and left)? Thanks Abel ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

1 0

reorient MRI volume
by abel cruz vadell 08 Mar '07

08 Mar '07

Hi everyone I have MPRAGE MRI volume acquired sagitaly and I need to convert it to axial. Could I do this task with any tool of FreeSurfer? Could I export back the result in analyze format? Thanks in advance Abel ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

2 1

smoothing error...?
by Cameron Ellis 08 Mar '07

08 Mar '07

Hi, After sphreical resampling I attempted to smooth the spherical surface which seemed to work fine but when I try to perform a group average using the smoothed surface I receive this error: troy:cameo[99] isxavg-re-sess -group Controlssh+smvsnh -sf sessidcontrolsshvsnh -df sesspar -a retrievalSPMHRF_sphere -c sh+smvsnh -space sphsmooth Log file is /autofs/space/troy_003/users/retrievalnewest/log/isxavg-re-sess-retrievalSPMHRF_sphere-sh+smvsnh.log Thu Mar 8 14:17:54 EST 2007 --------------------------------------------------- /autofs/space/troy_003/users/retrievalnewest isxavg-re -i /autofs/space/troy_003/users/retrievalnewest/SM0C1/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C2/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C3/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C4/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C5/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C6/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C7/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C8/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C10/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C11/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C12/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C13/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C14/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C15/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C16/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C17/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C18/bold/retrievalSPMHRF_sphere/sphsmooth/h -cmtx retrievalSPMHRF_sphere/sh+smvsnh.mat -avg Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/avg -std Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/std -sig Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/sig -t Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/t -minsig Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/minsig -iminsig Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/iminsig --------------------------------------------------- cat: /usr/local/freesurfer/stable/fsfast/docs/version: No such file or directory@: Expression Syntax. ERROR: nslices of /autofs/space/troy_003/users/retrievalnewest/SM0C1/bold/retrievalSPMHRF_sphere/sphsmooth/h ERROR: troy:cameo[100] I noticed that the smoothed spherical surface volume contains 1 more slice than the original resampled spherical volume, 7 instead of 6 in the h-lh-offset.bhdr file. Can someone explain to me why this would be, if this is related to this error, and offer a suggestion for correcting this? Thanks for anyone's assistance in advance! (working in stable environment) Cameron

2 1

omnibus contrast / paint-sess
by Sheeva Azma 08 Mar '07

08 Mar '07

Hello, I am trying to create and view an omnibus contrast for one subject. When I type the appropriate command: paint-sess -analysis SNgamma -contrast omnibus -space sph -spacedir sphsm20 -d . -s sub28a -subject sub28_recon I get the following error: ----------------------------------------------------------------- paint-sess logfile is /autofs/space/perun_004/users/sheeva/fMRIanal/log/paint-sess.log ----------------------------------------------------------------- setenv SUBJECTS_DIR /space/perun/3/users/cylix/Subjects INFO: painting onto white grep: /autofs/space/perun_004/users/sheeva/fMRIanal/sub28a/session.info: No such file or directory SpaceDir is sphsm20 SpaceSubDir is sphsm20 INFO: setting srcsubject to ico ------ lh hemisphere ------ Thu Mar 8 13:12:00 EST 2007 SpaceDir is sphsm20 INFO: Painting onto sub28_recon ERROR: cannot find any files with /autofs/space/perun_004/users/sheeva/fMRIanal/sub28a/bold_SN/SNgamma/sphsm20/omnibus/sig-lh It seems that stxgrinder-sess created fsig, f, iminsig, and minsig files, but did not create t or sig files. This only occurred for the omnibus -- it didn't happen with the other contrasts. I don't know if I should be doing something differently for the omnibus as compared to the other contrasts -- any insight would be greatly appreciated. Thank you! Sheeva Azma FREESURFER_HOME: /usr/local/freesurfer/stable Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070308 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp i686 NMR Center info (/space/freesurfer exists): machine: perun SUBJECTS_DIR: /space/perun/3/users/cylix/Subjects PWD: /autofs/space/perun_004/users/sheeva/fMRIanal

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