Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30061 discussions

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by ruth.smans＠med.kuleuven.ac.be 26 Nov '04

26 Nov '04

Hi, My name is Ruth Smans and I am new phd student learning how to work with FS (2003). I have come across a problem in coregistration when overlaying my functional images on my flattened anatomical, (both converted from SPM). My functional images include only 40 slices from the posterior part of the brain while my anatomical is a whole brain image. While I coregister the anatomical and functional images in SPM, when I try and overlay them in freesurfer the activations are moved forward. I assume I have to complete some form of manual coregistration using tkregister but I have been unable to open this. Could someone provide me with some information about commands for tkregister and how I can properly coregister the two images? All your help would be greatly appreciated. Thanks Ruth Smans

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mkbrainmask-sess failed
by Jia Liu 23 Nov '04

23 Nov '04

Dear all, When I used mkbrainmask-sess, an error occurred shown below. I am using the latest FreeSurfer, and the bet command is included in the distribution. Could anyone tell me how to fix it? thanks, Jia ++++++++++++++begin of error message+++++++++++++++++++++++++ mkbrainmask-sess 20041007syhu $Id: mkbrainmask-sess,v 1.2 2003/10/01 21:54:43 greve Exp $ Linux zion 2.4.22-1.zion #5 SMP Sun Dec 21 12:35:17 CST 2003 i686 i686 i386 GNU/Linux Tue Nov 23 20:23:19 CST 2004 /nfs/home/jliu/data/scramface/mystudy -sf sessid_syhu -df sesspar ProjectDir /nfs/home/jliu/data/scramface/mystudy ------------------------------------------------ ------------------------------------------------ /nfs/home/jliu/data/scramface/20041007syhu Tue Nov 23 20:23:19 CST 2004 /nfs/home/jliu/data/scramface/20041007syhu/bold mkbrainmask -i 005/f -o masks/brain -thresh 0.1 -umask 2 Scratch Dir is /tmp/mkbrainmask_4734 # ---------- Converting bvolume to .img ------------------ # mri_convert 005/f_000.bshort /tmp/mkbrainmask_4734/f.img Reading 005/f_000.bshort ... Reading 005/f_001.bshort ... Reading 005/f_002.bshort ... Reading 005/f_003.bshort ... Reading 005/f_004.bshort ... Reading 005/f_005.bshort ... Reading 005/f_006.bshort ... Reading 005/f_007.bshort ... Reading 005/f_008.bshort ... Reading 005/f_009.bshort ... Reading 005/f_010.bshort ... Reading 005/f_011.bshort ... Reading 005/f_012.bshort ... Reading 005/f_013.bshort ... Reading 005/f_014.bshort ... Reading 005/f_015.bshort ... reading from 005/f_000.bshort... INFO: bvolumeRead: min = 0, max = 885 TR=1.50, TE=30.00, TI=30.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -0.996195, 0.0871557) k_ras = (-0, 0.087156, 0.996195) writing to /tmp/mkbrainmask_4734/f.img... Analyze Output Matrix -3.125 0.000 -0.000 100.229; 0.000 -3.113 0.418 99.376; 0.000 0.272 4.782 -50.897; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 3 # ---------- Using FSL's BET to Extract Brain------------------ # This program has not been compiled for this data type /nfs/home/jliu/data/scramface/20041007syhu/bold bet /tmp/mkbrainmask_4734/f /tmp/mkbrainmask_4734/brain -m -f 0.1 ERROR: bet failed ERROR: mkbrainmask failed +++++++++end of error message++++++++++++++++++++

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mri_fill
by Calabrese Massimiliano 22 Nov '04

22 Nov '04

Hi everybody, I'm trying to fix a problem and I would be very happy if someone has an advice for me :) In some case I get an error about finding Corpus Callosum. So I have tried mri_fill -cc-xyz X Y Z and it seem to work. Now can I use recon-all to go ahead? (I really don't know if I'm able to use every single command like mri_tessellate... inflate etc) If yes which kind of recon I have to run? Massimiliano

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Re: [Freesurfer] thresh_zstat1.img
by Joongnam Yang 19 Nov '04

19 Nov '04

Hi all, In TkSurfer, is there a way of saving *.w files (or any other images for that matter) into a printable format, so that I can print them out? Thanks. Nam.

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Re: [Freesurfer] thresh_zstat1.img
by Evelina Busa 19 Nov '04

19 Nov '04

Hi If you are new to fMRI then it's likely you will be dissatisfied with the level of exchange on the freesurfer mailing list. Might we recommend several excellent online sources for NMR neophytes? This seems like a good one with links to some very active fMRI research centers: http://www.functionalmri.org Thanks, good luck! On Fri, 19 Nov 2004, Joongnam Yang wrote: > > Did you visually check the registration of the functional to the > structural? > > The registration using tkregister2 produces three files > func2struc.mat > func2struc.hdr > func2struc.img, > > I've tried to load func2struc.hdr in TkSurfer, but it crashes. > Again, I don't understand what you do when you "visual check" registration. > I am new to fMRI, please be more specific. > > Thanks. > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > --

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Re: [Freesurfer] thresh_zstat1.img
by Joongnam Yang 19 Nov '04

19 Nov '04

Thanks, Kevin > Have you tried changing the threshold parameters, in the > View->Configure->Overlay dialog box? The manual is very coarse on that. I've tried various combinations of the three parameters there. If you know the rule of combination, Please let me know. Nam.

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Re: [Freesurfer] thresh_zstat1.img
by Joongnam Yang 19 Nov '04

19 Nov '04

> Did you visually check the registration of the functional to the structural? The registration using tkregister2 produces three files func2struc.mat func2struc.hdr func2struc.img, I've tried to load func2struc.hdr in TkSurfer, but it crashes. Again, I don't understand what you do when you "visual check" registration. I am new to fMRI, please be more specific. Thanks. Nam.

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thresh_zstat1.img
by Joongnam Yang 19 Nov '04

19 Nov '04

Hi all, I did, (1) use mri_vol2surf to convert thresh_zstat*.img into thresh_zstat1-lh.w (2) use the *.w file to overlay it onto flattened surface. The resulting overlaid image (TkSurfer) doesn't show as much activation as that of thresh_zstat*.img (in FEAT). I see only a few tiny dots, not large areas of activation. Coud someone tell me in which direction I should explore it further? Nam.

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mri_vol2surf *.mat not found
by Joongnam Yang 18 Nov '04

18 Nov '04

For the mri_vol2surf, mri_vol2surf --src thresh_zstat1.img --src_type analyze --srcreg func2struc.dat --hemi lh --projfrac 0.5 --out ./thresh_zstat1-lh.w --out_type paint I got the following complaint. INFO: could not find XXX/XXX/thresh_zstat1.mat file for direction cosine info. Could someone tell me how to create *.mat for each statistical functional image? In other words, for each thresh_zstat*.mat? Thanks. Nam.

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Error in Sphere
by Calabrese Massimiliano 18 Nov '04

18 Nov '04

Hi everybody, does anyone give me an advice, please. I don't want to loose this subject at the end. Can I skip this step or can I try to fix it? Thanks a lot Massimiliano INFO: SUBJECTS_DIR is /net/apollo/nib/calabrem/freesurfer/subjects INFO: starting per-hemisphere operations ----- Starting Hemisphere lh -------- --------------------------------------------- Sphere lh Thu Nov 18 13:53:15 EST 2004 /net/apollo/nib/calabrem/freesurfer/subjects/gallagher/scripts mris_sphere -w 0 /net/apollo/nib/calabrem/freesurfer/subjects/gallagher/surf/lh.inflated /net/apollo/nib/calabrem/freesurfer/subjects/gallagher/surf/lh.sphere using write iterations = 0 Segmentation fault (core dumped) ERROR: mris_sphere exited with non-zero status

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Freesurfer