Freesurfer November 2004

freesurfer@nmr.mgh.harvard.edu

22 participants
53 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

4 3

wmfill
by Margaret Duff 06 Dec '04

06 Dec '04

Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret

3 13

setting the talairach origin
by Goldman, Aaron (NIH/NIMH) 30 Nov '04

30 Nov '04

Hi, I was wondering if there was any way in freesurfer to set the talairach origin manually. For a couple subjects, I've had bad transforms due to misplaced origins (one was down in front of the pons, for example). Thanks, -Aaron-

3 2

make several into one
by Joongnam Yang 30 Nov '04

30 Nov '04

Hi all, I have 8 flattened overlay images (overlay between structural and functional images). Is there a way of combining those images into one image, so that each activation can have different colors in one image? Any comments would be apprecaited. Nam.

2 1

statistical tools in freesurfer
by Glenn Lawyer 30 Nov '04

30 Nov '04

Hi, Is there any documentation for the statistical tools available with Freesurfer? We'd like to do a case/control study on cortical thickness and/or curvature in schizophrenia, the type of study mentioned in ^5 Fischl, Bruce, and Dale, A.M., (2000). Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images. We are able to generate the thickness, curvature, and spherical surfaces from our scans, the question is how to analyze the output. I understand that there are lots of ways to use Freesurfer with fMRI data, specifically the close link with FSL (FEAT and MELODIC are mentioned once or twice) and all those nice little programs in the $AFNI_DIR (which aren't mentioned in the Freesurfer documentation in any obvious place). Our study, however, is morphological, not functional. We could consider using FSL/SIENAX to get measures of brain atrophy between case/control, and then map this data onto the Freesurfer cortical surfaces, except then one wonders why we bothered processing all of our scans with Freesurfer (we could display the SIENAX output on Bert's brain, if Freesurfer is only used as a renderer). Further, this doesn't give information on changes in curvature. Nor is it certain that the two measures are equivalent (though in an ideal world they should correspond, both measure changes in white matter in the cortex). Also, I'm not sure if the SIENAX output is directly compatible with Freesurfer in the way that FEAT is. Thanks, +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +46 73 725 0730 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

3 2

(no subject)
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

1 0

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++++++++++++++++++++

1 0

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

2 1

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.

3 2

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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Freesurfer November 2004