Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

mri_convert and recon-all
by Sameer Walawalkar 14 Mar '07

14 Mar '07

Hello, I have two questions. 1> I am following instructions from http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-platform-releas… Under GETTING STARTED WITH YOUR OWN DATA there are two directives: cp -r <path_to_dicoms>/95555-2-*.dcm 001/ cp -r <path_to_dicoms>/95555-3-*.dcm 002/ with special note: . Note that in your own case, the name of the dicom files will be different (in this example, 95555-2-*.dcm consisted of 128 files). My MRI data is essentially a directory (directory name is a many digit number like 123456789) with four subdirectories named 1, 2, 3 and 4. So I have used the following commands cp -r <path_to_dicoms>/12345..../1/*.dcm 001/ cp -r <path_to_dicoms>/12345.../2/.dcm 002/ This is because directories 2 and 3 have 256 slices whereas 1 and 4 had six slices. (this could change from subject to subject) After that I do mri_convert -it dicom -ot mgz 001/ 001.mgz mri_convert -it dicom -ot mgz 002/ 002.mgz Is this correct procedure? This does create the .mgz files. 2> After this, I gave the command recon-all -autorecon-all -subjid <subjid> and this has been running for many hours now (as warned on the website). It has already created slices and sets. My understanding is it will do just about everything INCLUDING triangulation which is used for BEM forward moderls using MNE. Is this correct? Thanks for your help. best, sameer

1 0

how to deal with the cortex surface?
by duhanjian 14 Mar '07

14 Mar '07

hi ,I don't how to render the surface from A picture to B picture in SUMA? look carefully,the cortex surface is different,and I want to B effect.so does anyone has idea to deal with it?Thank you! 本邮件附件清单如下： (1) A picture.JPG (26.6 K) (2) B picture.JPG (26.8 K) duhanjian，duhanjian(a)sohu.com 2007-03-15

1 0

MGZ image format
by nayoung＠cis.jhu.edu 14 Mar '07

14 Mar '07

I put in my 161 x 191 x 151 Analyze image into Freesurfer and get 256 x 256 x 256 MGZ image. I need to make the scan back to my original .img format with original image size. I ran mri_convert and it gives me an image size of 256 x 256 x 256 or I tried -like option and it interpolates the data which I do not want. Thank you. Nayoung

1 0

use modified annotation file for parcellation
by Leila BH 13 Mar '07

13 Mar '07

Hello, I modified the annotation file rh.aparc.annot to 'rh.myaparc.annot' I can read it with read_annotation.m and it seems correct. (The modification is simply a subdivision of the middletemporal to 32 subregion named : middletemporal_1 .middletemporal_32). I copied this 'rh.myaparc.annot' file to /usr/local/freesurfer/sibjects/fsaverage/label/rh.myaparc.annot (I did this because the original 'rh.aparc.annot' file was there. When I run the mris_ca_label as done in the log file generated by recon-all command: mris_ca_label chuv44 rh ../surf/rh.sphere.reg /usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot ../label/rh.myaparc.annot I have an error: GCSAread(/usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot): file magic #28002 != GCSA_MAGIC (ababcdcd) mris_ca_label: could not read classifier from /usr/local/freesurfer/subjects/fsaverage/label/rh.myaparc.annot How can I do to use this annotation file? Is it necessary to have GCS file for parcellation? If yes how can I create it with this annotation file. I don't want to create my own atlas, I want to use the freesurfer atlas (35 entries) but just divide some of its regions. If needed, I can send you my annotation file. Thanks a lot

3 4

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

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