Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30096 discussions

working file system and mri_convert of the sample data
by Nam, Euicheol 03 Apr '06

03 Apr '06

Hi, I am practicing freesurfer with the sample data downloaded from freesurfer wiki homepage. I have two questions. 1) My computer doesn't have enough memory capacity, so I saved the data on my USB memory, but I couldn't find how to make freesurfer work with the data in the USB memory drive. Is it possible? According to the tutorial, I have to move the data to FREESUFER_HOME directory of my laptop Linux system. 2) Thus, I moved the sample data to FREESURFER_HOME directory in my computer hard drive but I found another problem in doing mri_convert data. The given sample data was, " buckner_data-tutorial_subjs" I made directory as "mksubjdirs anon" then, cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs and setenv {SUBJECTS_DIR} ${PWD} But when I tried to convert files as the tutorial said mri_convert 014-anon/001.dcm ${SUBJECTS_DIR}/anon/mri/orig/001.mgz this command could not be executed and the error message came up "014-anon/001.dcm file or directory does not exist". I guess "anon" directory couldn't have any dcm files because I made the directory in FREESURFER_HOME. And actually I couldn't find any dcm files in the sample data. I'll appreciate if I can get help from you.

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RE: [Freesurfer] how to register subcortical segmentation with theoriginal image
by Durastanti, Valentina (NIH/NINDS) [F] 01 Apr '06

01 Apr '06

Hi, I'm trying to run -autorcon1 of a subject who has 3 mgz images but always came out an error about the motion correction. So I tried run the step using just 1 image and it has gone fine! Have you any suggestion about the reason? The images look good! Thanks Valentina

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Outputting reformatted images in freesurfer
by Salil Soman 01 Apr '06

01 Apr '06

Hi, I have 2 images loaded into freesurfer (1 as an overlay) with the images transformed using a .reg file. Is there a way in freesurfer to output each of the loaded images in the pose they are in after loading the .reg file? (so the pose of each image is the result of whatever transforms are applied to the images by the .reg file) The end result I'm looking for is that is both images are loaded into freesurfer with a reg file that applies no transforms, the images will be the same as though the original .reg file was used. Thanks, Salil Soman sal(a)bwh.harvard.edu

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new to Freesurfer
by Chacko Cherian 01 Apr '06

01 Apr '06

Hello there, I am a Graduate research assistant at a Neuroimage analysis lab.I am starting to use Freesurfer for image analysis at our labs.Could you please let me know about any prerequisites which I would need before starting to use this tool.(I presume Tcl would be gud to know).Your advice will help me a long way in my work Thanks in advance Take care Chacko Cherian. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Problem
by Tracy Abildskov 01 Apr '06

01 Apr '06

Hello, I just installed FreeSurfer following the instructions that were outlined on the web site. Now I am testing the installation also following the instructions on the web site. The following is the error that I got. [psyched@byu321453wks freesurfer]$ pwd /usr/local/freesurfer [psyched@byu321453wks freesurfer]$ tkmedit bert orig.mgz tkmedit: error while loading shared libraries: libtix.so.0: cannot open shared object file: No such file or directory [psyched@byu321453wks freesurfer]$ Are there other packages that I need to install to get freesurfer to run? Thanks, Tracy

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RE: [Freesurfer] lh.curv versus lh.curv.pial
by Durastanti, Valentina (NIH/NINDS) [F] 30 Mar '06

30 Mar '06

thanks Valentina -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, March 30, 2006 12:44 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] lh.curv versus lh.curv.pial depends on what kind of machine, but yes it can take that long (sorry) Bruce On Thu, 30 Mar 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > > Hi, > I've a question: I'm running the autorecon2 of some subjects and I > realized that they take more than 24 hours to finish it. Is it possible? > I know that the step can take upwards of 15 hours but I was wondering if > it is too much! > > Thanks > > Valentina > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RE: [Freesurfer] lh.curv versus lh.curv.pial
by Durastanti, Valentina (NIH/NINDS) [F] 30 Mar '06

30 Mar '06

Hi, I've a question: I'm running the autorecon2 of some subjects and I realized that they take more than 24 hours to finish it. Is it possible? I know that the step can take upwards of 15 hours but I was wondering if it is too much! Thanks Valentina

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contrast.mat file
by Sasha Wolosin 30 Mar '06

30 Mar '06

What format should my contrast.mat file be for group analysis? e.g. if my contrast vector is [1,-1], should the contrast.mat file be a text file with [1 -1] as the first line? or 1 -1 as the first line? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: Outputting reformatted images in freesurfer
by Salil Soman 30 Mar '06

30 Mar '06

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Talairach question
by Martin Ystad 30 Mar '06

30 Mar '06

Hi, I'm doing a group study and I have a question regarding the Talairach transform. I need to make a new transform for some of my subjects using the brainmask.mgz-volume. For others, the original transform is okay (visually) . Is it a problem to have some transforms based on the brainmask volume, and others made from the nu volume? Should I make new transforms for all subjects, even though some of the original ones are fine? Thanks, Martin Ystad University of Bergen, Norway.

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