Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

How to analysis animal data
by lan lin 20 Jul '07

20 Jul '07

I know someone here have successfully apply freesurfer on monkey. Do you mind to describe how you can do that? Freesurfer is closely related to human atlas. If you need to apply it on animal, like monkey, do you need to contruct a monkey atlas? Anything besides atlas that need to take care? thanks

2 1

Intersecting surfaces (thickness = 0mm)
by Inge K. Amlien 20 Jul '07

20 Jul '07

Hello list, when I process on v3.05 I notice areas where the pial and wm surfaces intersect, giving cortical thickness = 0. This is usually seen in the medial temporal area. Is this a known issue, and how should I deal with it? See attached screenshots. Have a nice day Inge Amlien Department of Psychology University of Oslo ------------------------------ Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 RedHat release: Red Hat Enterprise Linux WS release 4 (Nahant Update 5) Kernel info: Linux 2.6.9-42.0.10.ELsmp x86_64 (Hugging Linux)

2 1

mris_volmask
by Ipek Oguz 19 Jul '07

19 Jul '07

Hi, Where can I get the mris_volmask tool? I've seen that it was on the ftp server under pub/dist at some point, but it seems to have disappeared. Thanks a lot! -ipek

2 1

recon-all Is-Running
by Doug Greve 19 Jul '07

19 Jul '07

I've just added a new feature to the dev version of recon-all to help you manage your processes. When you launch recon-all, it will create a file called IsRunning.lh+rh in your subject/scripts folder. When recon-all finishes (with or without errors), this file will be deleted. So, the presence of this file indicates that recon-all is being run on this subject. This file may also exist if recon-all died in a way that it could not clean up (eg, control-C). The contents of the file indicate information about the process that will allow you to determine whether it is still running or not: date Thu Jul 19 19:24:30 EDT 2007 processid 10196 hemi lh rh host icebox user greve Linux icebox 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux You can then ssh to the host and use the unix 'ps' command to check for the existence of the process. If you run recon-all on this subject again while this file exists, it will exit indicating that the subject is already being processed or recon-all died uncleanly. If you want it to run regardless, then add -no-isrunning to the command-line. It will not delete the IsRunning file, just ignore it. When you run the hemispheres separately (ie, -hemi lh or -hemi rh), it will create a IsRunning.lh or IsRunning.rh file. This allows you to run recon-all for both hemis in parallel. If this file exists or IsRunning.lh+rh exists, then again recon-all will exit telling you that the subject is already being processed or recon-all died uncleanly. doug -- 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

1 0

gca file format
by lan lin 19 Jul '07

19 Jul '07

I got some question about gca file format. What does totaltraining means? GIBBS_NEIGHBORS is more 6 neighboring voxels. What is relationship between them? From 1:6 , which one is left, right etc? thanks

1 0

opening aseg.stats file
by Lindsay Casmaer 19 Jul '07

19 Jul '07

Hello all, I am finally gearing up to look at the stats generated from processing. Though when I open the stats file as a tab/space delimited in excel, it really looks messy. Any other programs that would be good to view the tables with? Thanks. -Lindsay

2 1

one list thing
by Bruce Fischl 19 Jul '07

19 Jul '07

if you could include the funding source (particularly NIH institutes!) that would be great.

1 0

mri_glmfit
by Lars M. Rimol 19 Jul '07

19 Jul '07

Hi, Please ignore my previous mail, I did not see that "external" on the y axis means dependent variable (blame it on the early morning blues...) -- yours, LMR

1 0

clarification
by Bruce Fischl 19 Jul '07

19 Jul '07

Two more thing: please include the # of subjects that you have analyzed, and any clinically relevant study that uses FreeSurfer can be included (included DTI and fMRI). thanks again, Bruce

1 0

mri_glmfit
by Lars M. Rimol 19 Jul '07

19 Jul '07

Hi, I ran mri_glmfit with a fsgdf looking (in principle) like this: GroupDescriptorFile 1 Title MyTitle Class Group1 plus blue Class Group2 circle green Variables ICV Input subjid1 Group1 10000 Input subjid2 Group2 20000 Dependent variable iscortical thickness. When I "load group descriptor file", i.e. y.fsgd, and click on a vertex and choose "View by class", the button to the right of that has only one level: "ICV", and the x axis of the graph also has the title ICV (and units that seem to represent ICV). However, I am interested in visualising the dependent varable cortical thickness per vertex, not the continuous predictor/regressor ICV. Have I made a mistake in the fsgdf? Thank you! -- yours, LMR

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