Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

Sever problem
by Jürgen Hänggi 22 Jan '10

22 Jan '10

Dear FS experts I tried to download the Mac distributions of FS, but there seems to be a server problem, although the Linux distributions can be downloaded. Thanks Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Orientation of 001.mgz versus raw dicom data
by yzhangd＠artsci.wustl.edu 21 Jan '10

21 Jan '10

I have run the following command to create a 001.mgz file from raw *.dcm data: recon-all -s <subjid> -i <path to *.dcm data> The output 001.mgz file is not in the same native space as the original *.dcm data. Could anyone tell me what space the 001.mgz file is in? Does the above command change the orientation (i.e does it rotate/translate) besides simply converting from .dcm to 001.mgz thanks a lot yuning

3 2

license problem
by Guang Zeng 21 Jan '10

21 Jan '10

Hi, there, I installed FreeSurfer under my local directory few months ago. Last week, I copied all the FreeSurfer folder under my local directory (include .license file) to the /home directory of our group, so everyone can use it. However, it turns out that they can not use it even they can see the .license in the /home directory through their machine. So do I need reinstall Freesurfer under our /home directory, instead of just copy? Thanks! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/196390708/direct/01/

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commandline tools to create .mgh files from .nii files.....
by Ritobrato Datta 21 Jan '10

21 Jan '10

Hello All, Are there commandline tools to take processed functional data in .nii format and overlay it on the inflated or spherical surface and output a .mgh file ? I want to specify the registration method as "Calculate identity matrix" Thanks Rito

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mri_vol2surf
by 丽孔 21 Jan '10

21 Jan '10

Hello developer, I want to change a structure MRI (*.img) into two surface files (*_R.w and *_L.w). I first use mri_convert to change *.img to *.mgh ; then use mri_vol2surf to change a *.mgh file to two surface files *_L.w and *_R.w. But here I meet a problem: I don’t know how to get the register.dat file. I search many documents about this problem, But still didn’t find a method for this problem. Expecting freesurfer advancer give me some instructions! Any help will be appreciated! Best regards! karry ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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Flip surface model
by Jürgen Hänggi 21 Jan '10

21 Jan '10

Dear FS experts As far as I know from Doug, there are preliminary tools for flipping a surface model (reversing left and right hemisphere) http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11896.html Because these tools are not yet available I would like to know whether you would recommend to flip the raw MR image and the running recon-all on this flipped MR image. Thanks in advance Best regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

3 2

flag error
by Buchmann Andreas 21 Jan '10

21 Jan '10

Dear Freesurfer Experts, after a new installation of freesurfer, the command "tkmedit" worked, but with the command "recon-all -i ... -s ..." we ran into the following error: Flag i unrecognized. i /Users/michael/Desktop/K01.img s K01 Darwin Macintosh-3.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all exited with ERRORS at Thu Jan 21 08:17:06 CET 2010 Any suggestions, what the problem might be? Best regards and thanks in advance Andreas

2 1

Mri_glmfit, paired analysis protocol
by Stidd, Reva (NIH/NIMH) [F] 20 Jan '10

20 Jan '10

Hi there, I'm trying to compare a sample with a T1 and T2 for each subject using the paired analysis protocol. I've completed everything *except* for the mri_glmfit step without error. I think it might have to do with the way my second FSGD file was created/saved. The command I'm entering and the subsequent error message is below: CHP-MP6:subjects revastidd$ mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C intercept.mtx --glmdir lh.longitudinal_age.glmdir gdfReadHeader: reading paired-diff.fsgd ERROR: FSGDF version 0 unsupported (paired-diff.fsgd) CHP-MP6:subjects revastidd$ My paired-diff.fsgd file was made in TextEdit: GroupDescriptorFile Class Main Variable Gender Input sub1pair Main 1 Input sub2pair Main 1 Input sub3pair Main 0 Input sub4pair Main 0 Input sub5pair Main 1 Input sub6pair Main 1....... FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Kernel info: Darwin 9.8.0 i386 Current Working Directory: /Applications/freesurfer/subjects Which freesurfer: /Applications/freesurfer/bin/freesurfer Please let me know if you need anything else! Thank you so much, -Reva

2 1

WM.mgz corrections in the ventricles & Individual Normalization
by Sherri Novis 19 Jan '10

19 Jan '10

Hello - I have two questions: 1) I noticed on wm.mgz volumes that were segmented properly, that even when the ventricles were automatically filled in, on some slices they are somewhat patchy (partially filled in with white, with some black/blank voxels). Do these patchy wm fill-ins require manual fill-ins to make them entirely opaque? I went through the tutorial, and it was not clear whether a patchy fill-in required a correction or not. 2) What is the best automated measurement that can be used to normalize an individual's cortical segmentation volumes for between subject comparison? We have been using gray+white volumes (why we need the ventrical volume processing to be consistent) - but not sure if ICV would be better individual normalizer. Thank you for your time - Sherri

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FreeSurfer two atalses
by Guang Zeng 19 Jan '10

19 Jan '10

Hi, there, Are there any place in FreeSurfer Wiki or journal paper explain why FreeSurfer need to atlases; Subcortical and Surface? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/

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Freesurfer January 2010