Freesurfer December 2008

freesurfer@nmr.mgh.harvard.edu

65 participants
107 discussions

Command Not Found
by Christian Lambert 15 Dec '08

15 Dec '08

I'm just starting out with freesurfer. I am using CentOS5 Linux shell on a windows machine using Freesurfer V4.1.0 with the monitor settings on 32bit. I have set up the license file and also configured freesurfer as per the wiki pages: [user@localhost ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Desktop/freesurfer FSFAST_HOME Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR Desktop/freesurfer/subjects MNI_DIR Desktop/freesurfer/mni Now when I run recon all (using my own data) I get the following error message: Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /home/user/Desktop/freesurfer/subjects Actual FREESURFER_HOME /home/user/Desktop/freesurfer Linux localhost.localdomain 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:33:52 EDT 2008 i686 athlon i386 GNU/Linux mri_motion_correct.fsl: Command not found. flirt: Command not found. talairach_avi: Command not found. tkregister2_cmdl: Command not found. nu_correct: Command not found. mri_normalize: Command not found. .... ... .... mris_make_surfaces: Command not found. mris_register: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. cp: cannot stat `Desktop/freesurfer/bin/recon-all': No such file or directory /home/user/Desktop/freesurfer/subjects/chris2 mri_watershed: Command not found. I have been through the manual, wiki pages and seached the mailing list extensively but could not find a solution to this problem. I notice one similar thread in 2006 but it never detailed how the problem was solved, but based on that I include the line below: [user@localhost ~]$ ldd 'which mri_convert' ldd: ./which mri_convert: No such file or directory Thanks for any insight you can provide.

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cortical parcellation and local maximum
by Maartje Katzenbauer 15 Dec '08

15 Dec '08

Dear Freesurfer, I have two questions. My first question is about the cortical parcellation. It's possible to make an aparcstats2table for the hemispheres on the paramaters volume, thickness, area and mean curvature. I would like to know the total gray matter volume, because I want to know if I need to correct for it, like we do in volumetry studies. One needs to correct for intracranial brainvolume differences between specific groups. I can't find the total gray matter volume in the aparcstats2table for volume. And I can't figure out how I can destilate it from QDEC. My second question is about de brainpicture in QDEC. If you have set your threshold and you define a ROI, I would like to know the 'local maximum' in the colored area. (You can set the arrow manually by changing the threshold maximum to a level that the color keeps on changing). But I would like to find a structured and more reliable way. Does anybody know if it's possible? Thanks a lot. Kind regards, Maartje Katzenbauer

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Recommended hardware configurations?
by Matt Cain 13 Dec '08

13 Dec '08

Greetings, I've been trying to analyze a rather large data set (6 runs of 84 volumes of 128x128x28) and I've been running into out of memory errors with selxavg3-sess. These seem to be similar to those reported previously: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-May/007649.html Watching my system resources as I run, it looks like I'm hitting Matlab's 2GB memory ceiling, even when using the -float and -perrun options. We're looking into getting a new analysis machine and we're thinking an x64 machine might help us get around this. Are there any recommended or suggested configurations for using FreeSurfer and FS- FAST on large data sets? Thanks, -Matthew S. Cain mcain(a)berkeley.edu

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metric distortion definition
by Michael Harms 12 Dec '08

12 Dec '08

Hello, How is the distortion calculated by 'mris_jacobian' defined? Based on this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05419.html I'm guessing that the output of mris_jacobian lh.white lh.sphere.reg lh.jacobian_white is identical to the "metric distortion" measure used in Wisco et al. 2007; i.e., area of a triangle on lh.sphere.reg divided by area of a triangle on lh.white, normalized for the total surface area of each surface (which is done automatically by 'mris_jacobian' unless you specify the -noscale flag). Is this correct? If so, the Wisco (mris_jacobian) definition of "metric distortion" seems quite different from what is used in the energy functionals that control the inflation and registration processes, where the term for metric distortion is defined using the distance between corresponding vertices in the two surfaces. Is there some relationship between these two different definitions of distortion? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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mri_segstats program omitted from MacOSX Leopard Intel download package.
by Greg Harris 12 Dec '08

12 Dec '08

Nick, We have yet another request regarding the MacOSX Leopard Intel version 4.1.0 download package that delivers FreeSurfer. The program mri_segstats is not found, although it is there in the Linux package. Also, recon-all -segstats gives the 'switch not recognized' error message in MacOSX Leopard Intel, but accepts it in the recon-all in the Linux package. I also noted that the fswiki/ReleaseNotes tells us to run recon-all -segstats -wmstats, but there is no -wmstats; what you need is -wmparc. Until you can post the updated files, probably mri_segstats and recon-all, we will have to avoid FreeSurfing on our Macs which number about half of our compute cluster. Thanks for your help! Greg Harris Iowa Psychiatric NeuroImaging Consortium Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.

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Automated subcortical labeling : what is the RB_all_2006-2-15 atlas?
by Julien Dubois 12 Dec '08

12 Dec '08

Hi freesurfer developers I'm working with freesurfer's subcortical anatomical labels. I understand that they are based on a database of manually labeled anatomical scans, which were normalized to the MNI template in order to get probability maps, that freesurfer uses as prior information. In a slide (in freesurfer.recon.2007.ppt I believe) there is a line that says the atlas is RB_all_2006-2-15. What is this particular atlas based on? how many brains were manually labeled? I couldn't find any reference for this atlas. There exist some probabilistic cytoarchitectonic maps (cf Eickhoff NeuroImage 2005). I understand that freesurfer only makes use of manually labeled MRI scans, not cytoarchitectonic information. Is that right? how hard would it be to use the probabilistic cytoarchitectonic atlas instead of RB_all_2006-2-15? is it doable at the user level or does it require messing around with the code? Thank you very much in advance! - Julien

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QDEC data into FSL
by Alexandru Hanganu 12 Dec '08

12 Dec '08

Hello All, Can you please tell me, when we get the results from QDEC {$SUBJECTS_DIR/qdec/Untitled/lh-Avg-thickness-age-Cor/sig.mgh} how can we threshold the image and include it as a seed into FSL tractography ? What command line should I use ? Thank you for your help, Best regards, Alexandru Hanganu. ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.

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libXss ?
by Siddharth Srivastava 11 Dec '08

11 Dec '08

Hi surfers, I am trying to understand the source of the following errors. I know it was not able to locate libXss, but why should mris_volmask need libXss ? I have been told it is a library used by X sceensaver -------------------------------------------------------- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance RO58NormJB mris_volmask.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Linux compute-0-3.local 2.6.18-53.1.14.el5 #1 SMP Wed Mar 5 11:37:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Dec 8 00:47:13 PST 2008 ------------------------------------------------------------ best regards, sid. On Thu, Dec 11, 2008 at 3:09 PM, Michael Harms <mharms(a)conte.wustl.edu>wrote: > > Hello, > I'm curious, what algorithm is used for setting the "mid" and "max" > threshold values in QDEC when using the "Set Using FDR" button? > > And, what does the algorithm do for setting the "min" threshold when no > single p-value is significant enough to satisfy the necessary inequality > for the specified FDR Rate? > In that case, is the resulting "min" just set to the -log10(p) of the > most significant p-value? > > If easy to implement, it would be handy if the output to the terminal > reported the number of vertices with P < than the FDR determined "min" > threshold. > > cheers, > Mike H. > > > -- > Michael Harms, Ph.D. > -------------------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > Renard Hospital, Room 6615 Tel: 314-747-6173 > 660 South Euclid Ave. Fax: 314-747-2182 > St. Louis, MO 63110 Email: mharms(a)wustl.edu > -------------------------------------------------------------------- > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] Some questions about my analysis
by Nick Schmansky 11 Dec '08

11 Dec '08

Marie, Thanks for the info. I just updated the page: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI Nick On Thu, 2008-12-11 at 23:25 +0100, Marie Schaer wrote: > Nick, > > To run lGI, one need Matlab with the image processing toolbox > installed. Maybe we can add this info in the lGI wikipage? Thanks! > > Marie > > > > On 11 déc. 08, at 21:02, Nick Schmansky wrote: > > > Marie, > > > > Are any special toolboxes required in Matlab to run the lgi code? Or > > will plain matlab suffice? > > > > Nick > > > > > >> > >> 6) I would like to have a look at the local gyrification index aswell > >> but still need to buy Matlab for it. Do I also need some extra > >> toolboxes > >> to run the lgi calculation - or do I just need the core programm? > >> > >> Any help is greatly appreciated. > >> > >> Best wishes, > >> Christian Scheel > >> > >> > >> --- > >> University of Cologne > >> Department of Psychiatry > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > >

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qdec and left mouse button
by Michael Harms 11 Dec '08

11 Dec '08

Hello, In the QDEC in the current FS distribution (v4.1.0), attempting to rotate the surface (via left mouse button) automatically also opens the scatterplot of the individual values at the vertex where you clicked (or an empty plot if you click in the background). Is there a way to turn off this behavior, so that one can simply rotate the surface without the scatterplot opening and obscuring the screen? In the QDEC with previous FS versions (e.g., v4.0.2), one had to do Control+left mouse to get the scatterplot (which was fine by me)... cheers, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Freesurfer December 2008