Freesurfer October 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
61 discussions

Templates in Freesurfer
by Juergen Haenggi 24 Oct '06

24 Oct '06

Dear Freesurfer users we use Freesurfer for analyzing patients with different dementias. Because the brains are very atrophic we deliberate whether the implemented templates (MNI 305) are OK for an analysis of atrophic brains with Freesurfer. Any suggestion? Thanks in advance Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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TIV estimation using FreeSurfer
by Joao Pereira 24 Oct '06

24 Oct '06

Dear all, I have been trying to use the eTIV value FS outputs after the -autorecon1 and -autorecon2 stages, registering it in the aseg.stats file. The purpose would be to see how reliable that value is when compared to our own manual measurements. When reading the Buckner paper, I have noticed that a stringent requirement for optimal perfomance is the usage of an adequate template (i.e., age matched template), and I believe FS uses the MNI 305 template (at least in 2006 versions), which is not adequate for our population. My questions are: 1) Is it possible to build our own template and then introducing it in the FS package? If so, where? (please notice that I am not interested in surface templates) 2) If 1) is possible, is the TIV estimation hindered by such a procedure? I know you have adjusted the calculation of the eTIV using bootstrap, which means that you don't use a pure version of the atlas scale factor (ASF), but you scale it by a fixed number you've obtained with this adjustment. My guess is that this estimate will no longer be valid. 3) I have adjusted the initial transform outputs by using mri_total, T1.mgz, brain.mgz and, in some cases manual adjustments. This affected talairach.xfm. Is this the adequate approach for TIV estimation purposes? I remember reading something about talairach_with_skull.lta... Thank you very much for your patience and assistance! Regards, Joao Pereira

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Percent signal change: what stats to read
by raij＠nmr.mgh.harvard.edu 22 Oct '06

22 Oct '06

Hi, We have calculated a FIR group analysis with FS-FAST and have the corresponding ces, cesvar, f, fsig, iminsig, minsig, sig, and t maps in the contrast folders. Which one of these should I use for presenting % signal change? We want to do some further analyses of the group analysis results with matlab and would need to use % signal change as the input values for those analyses. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Freesurfer crash
by Wolf, Ingo 22 Oct '06

22 Oct '06

Hi everyone. I habe a rather obscure problem. After loading a volume with tkmedit, I tried to open the file menu via the file button in the menu bar and instanly freesurfer crashes. The software is installed on a Apple PowerMac OSX 10.4.6, Dual G5 2.5 GHz, Memory 2.5 GB. I wonder if this is a hardware problem? Thanks Ingo

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Re: [Freesurfer] posting a question again
by Joongnam Yang 20 Oct '06

20 Oct '06

Thanks, Doug, I never used mri_surf2surf, the latest version I downloaded. Would you be more specific on how to convert avg_thickness to the average subject? (I tried mri_surf2surf --srcsubject SUBJECT --tfmt avg_thickness, but it's asking a whole lot more variables...) Nam. >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 10/20/06 12:34 PM >>> Does it work if you don't use projfrac? We have a bug in the make_average_subject code that causes the average thickness (lh.avg_thickness) to be painted on the last subject in the list instead of the averaage subject. One work-around until we get this fixed is to convert the avg_thickness to the average subject with mri_surf2surf. This will require a new version of surf2surf, which you can get from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf Run it with --tfmt curv doug Joongnam Yang wrote: >Dear all, > >I've been waiting for an answer to the following question. > >I am trying to overlay group-averaged data (FSL) on an averaged anatomical >brain (Freesurfer). >I did the following, > >mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze >--srcreg register.dat --hemi lh --projfrac 0.5 --out >AVG.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint > >and got the following error message, > >MRISreadCurvature: could not open >/home/nam/AVERAGE/average/surf/lh.thickness >No such file or directory > >In the surf directory, I DID find "lh.avg_thickness". >I renamed "lh.avg_thickness" "lh.thickness", but it didn't work. >Would someone please let me know how to remedy this? > > > >>Nam. >> >> >_______________________________________________ >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

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Error running mri_ca_register in recon-all (v3.0.3)
by sliceofpy＠gmail.com 20 Oct '06

20 Oct '06

Hello, I am getting an error with mri_ca_register when running recon-all with -autorecon2 (ERROR: mri_ca_register with non-zero status), perhaps related to the one discussed here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03626.html I'm running freesurfer-Linux-centos4-stable-pub-v3.0.3 on FC4. This is a new installation so I haven't actually successfully run through recon-all on this machine yet. Attached is the recon-log file from today's run; let me know if any other info would be helpful. Any suggestions on sources for the error or how to further troubleshoot would be much appreciated. Thanks, Jonathan

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posting a question again
by Joongnam Yang 20 Oct '06

20 Oct '06

Dear all, I've been waiting for an answer to the following question. I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following, mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --out AVG.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint and got the following error message, MRISreadCurvature: could not open /home/nam/AVERAGE/average/surf/lh.thickness No such file or directory In the surf directory, I DID find "lh.avg_thickness". I renamed "lh.avg_thickness" "lh.thickness", but it didn't work. Would someone please let me know how to remedy this? >Nam.

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mri_convert --unwarp_gradient_nonlinearity
by Kuijer, J.P.A. 20 Oct '06

20 Oct '06

Hello all, I'm interested in correcting the geometric distortion introduced by the non-linearity of the gradients of our Sonata MR system. I noticed that mri_convert has an option to do this: --unwarp_gradient_nonlinearity When I try to use this option, I get an error message: INFO: unwarping ... Error: couldn't open /usr/local/bin/freesurfer/data/gradientNonlinearitySonata.mff So this file seems to be missing in the freesurfer distribution. Can I request that file somewhere, or is any software available to calculate it from the spherical harmonics as provided by Siemens? cheers -- Joost

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recon-all with more than one subject
by Juergen Haenggi 19 Oct '06

19 Oct '06

Dear Freesurfer users is there any possibility to run recon-all with more than one subject? what is the option to use several subjects within one recon-all command? can one use more than one -s option in one recon-all command? thanks in advance best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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FreeSurfer Coordinates
by Doug Greve 18 Oct '06

18 Oct '06

I've created a new set of powerpoint slides with info about FreeSurfer cooridnate definitions. You can find it at: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems 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

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Freesurfer October 2006