Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

3mm slices?
by Mishkin Derakhshan 25 May '10

25 May '10

Hi, I'm wondering if anyone has looked at the accuracy/reproducibility of cortical thickness measurements using 3mm slice data. I found the Han 2006 paper in NeuroImage comparing different sequences, but it doesn't compare different slice thicknesses. If not, does anyone have anecdotal experience using 3mm slices? thanks, mishkin

2 1

brainmask and wm correction
by Deniz Ozgen 25 May '10

25 May '10

Hello all, I am new to FreeSurfer and still trying to understand how things work. I am currently trying to understand how the manual correction works. Following the online tutorials I was able to fix the brainmask and wm.mgz, and also add control points in the wm so that low intensity wm is also included in the segmentation. In the tutorials it is suggested to run the FreeSurfer after doing the brainmask correction by recon-all -autorecon2 -subjid <subject name> After the wm control point addition, the tutorial says that "run the program with -autorecon2-cp" Is it possible to do brainmask correction, white matter edits and control points in one session and run the FreeSurfer again to fix all this at once? Is there a different command for this? I apologize if this has been answered before. Thanks a lot. Deniz.

2 1

MNI305 to MNI152
by Yigal Agam 25 May '10

25 May '10

How do I convert between the two coordinate systems? Yigal

1 0

Error untarring fsfast tutorial
by Jesse Friedman 25 May '10

25 May '10

Hi, I'm following instructions from: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialData The anatomical data extracts successfully, but the functional data hangs on this command: tar xvfz fsfast-tutorial.tar.gz The process extracts files for a while and produces this output: ./fsfast-tutorial/ ./fsfast-tutorial/.xdebug_tkmedit ./fsfast-tutorial/run-fsfast-tut.log.bak ...More successful extractions... ./fsfast-tutorial/fb1-preproc-study/mgh-104.1/bold/007/f.nii ./fsfast-tutorial/fb1-preproc-study/mgh-104.1/bold/007/fmcsm5.nii tar: Skipping to next header tar: Archive contains obsolescent base-64 headers (process hangs here) Any help? I'm in /autofs/space/schnook_001/users/caitlin_tutorial/functional. bugr details are below. Thanks! Jesse FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: vantz SUBJECTS_DIR: /autofs/space/ventzl_001/users/SUBJECTS_DIR PWD: /space/schnook/1/users/caitlin_tutorial/functional ssh vantz setenv SUBJECTS_DIR /autofs/space/ventzl_001/users/SUBJECTS_DIR cd /space/schnook/1/users/caitlin_tutorial/functional

3 4

Getting Talairach Coordinates
by Yigal Agam 25 May '10

25 May '10

Hi, Is there a way to get the Tal and MNI coordinates of a given fsaverage vertex through matlab or the unix command line, without opening tksurfer? Thanks, Yigal

2 1

Fractional Anisotropy Command Question
by Weisinger, Brian (NIH/OD) [E] 25 May '10

25 May '10

Hello, I am trying to run the dt_recon with the fractional anisotropy to do a project with white matter. I am running into a problem actually getting the command to work. I am trying to follow the example online dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti But I am not sure where/what I am supposed to put after the -i. The other stuff I am pretty sure I know, --s = the subject folder --o = the folder I want the output to go in Can you fill me in on what I'm missing, I looked in the subjects output files and could not find anything that ended with .dcm. I was told that it is the input diffusion weighted time series. Is that something that would be different for everyone or something that would always be the same? If it is unique for each person where would I find that file so I can input the name of it? Thank you, Brian Weisinger

2 1

Tutorial Files
by Yigal Agam 25 May '10

25 May '10

Hi, We're having problems untarring the tutorial data. Are the uncompressed data available anywhere? Thanks, Yigal

1 0

mris_preproc thickness vs functional data
by ridatta＠mail.med.upenn.edu 25 May '10

25 May '10

Hello All, I have a question regarding the actual command issued under the mris_preproc wrapper. I noticed that when I ran the recon-all -qcache to resample the different anatomical measures like thickness etc to fsaverage, one of the step is the following - mri_surf2surf --srcsubject 068 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval 068.1.mgh --sval ./lh.thickness --sfmt curv --noreshape --no-cortex When I ran mris_preproc using the tutorial as specified here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup the step similar to the one above is the following mri_surf2surf --srcsubject 068 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval 068.1.mgh --sval ./rh.VisStimBoth_rb.mgh --noreshape --no-cortex" What does the "--sfmt curv" do ? What happens if its included in the resampling of the functional data ? Should I ? Please let me know. Thanks Ri

6 5

error in simulation script
by johanna feiler 25 May '10

25 May '10

Dear FreeSurfer experts, I want to run the simulation script with qdec, but I always get the following error message: 'error in simulation script generation command failed: chmod u+x' and then the adress of the 'mri_glmfit-sim-mc-z.abs.2' - file. This it what the file contains: mri_glmfit-sim \ --glmdir /home/hiwibp14/smb4k/CORTICAL/fmrt/Studie43/freesurfer/qdec/Untitled \ --sim mc-z 10000 2 mc-z.abs.2 \ --sim-sign abs \ --overwrite What can I do to run my simulations? Any help is appreciated! Johanna Feiler ___________________________________________________________ GRATIS: Movie-Flat mit über 300 Top-Videos. Für WEB.DE Nutzer dauerhaft kostenlos! Jetzt freischalten unter http://movieflat.web.de

1 0

question about using control points
by Mehul Sampat 24 May '10

24 May '10

Hi Folks, One of my colleagues had the following issue while using control points. He re-processed the case after adding some control points (shown in the first figure), but after doing so, the WM was still not included. Is this a typical case, where it would be better to edit wm.mgz instead of adding control points. Second question: we noticed that some WM was left out from the yellow surface. But when we look at wm.mgz these values of these voxels are in the range 80-95 (shown in the second figure) In such cases should we remove these voxels from wm.mgz (using the right click option) and then include them again ? That is, this would change the voxel values from 80-95 to 255.. I ask this because sometimes, we see that the yellow surface is clipped but there is nothing to include in the wm.mgz since the corresponding values do have some intensity values Please let me know if you need more information/clarfication about the second question. thanks Mehul

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