Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30061 discussions

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

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Re: [Freesurfer] from volume to surface
by Joongnam Yang 03 Dec '04

03 Dec '04

Thanks, Doug, When you visually check the registration, using tkregister2 --s subjid --targ struc_fs_t1.img --mov YUNG070904_41.img --regheader --reg register.dat. two windows show up. Is there a source, or instructions, or manual, regarding what to do with the two winows? Nam.

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Re: [Freesurfer] from volume to surface
by Joongnam Yang 03 Dec '04

03 Dec '04

Thanks, Doug, By any means, does the following register.dat look incorrect? subjid 3.800000 5.000000 0.150000 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 -1.525879e-05 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 round Nam.

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Re: [Freesurfer] from volume to surface
by Joongnam Yang 03 Dec '04

03 Dec '04

Sorry, Doug Here is the full command and log with segmentation fault. Nam. ================== mri_vol2surf --src FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --surf occip.patch.flat --out ./thresh_zstat1-lh.w --out_type paint INFO: output format is paint srcvol = FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.img srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = occip.patch.flat hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.img ----------------------------------------------------------------- INFO: could not find FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).INFO: if not valid, please provide the information in FMRIDATA/FUNC/YUNG070904_41.feat/thresh_zstat1.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 5.52912 Done loading volume Reading surface /home/nam//blobby/surf/lh.occip.patch.flat Segmentation fault (core dumped) =========================

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from volume to surface
by Joongnam Yang 03 Dec '04

03 Dec '04

I have a functional volume, and a surface (occipital lobe cut, not the whole cortext) and I want to create *.w file using mri_vol2surf. mri_vol2surf gives me "segmentation fault", probably because the volume and the surface do not match. Could someone give me a clue on how to create a *.w file using mri_vol2surf when functional is whole and anatomical is only partial surface of the whole cortex? Thanks in advance. Nam.

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ROIs
by aleontie＠meded-mail.ucsd.edu 01 Dec '04

01 Dec '04

Hi, > I'm trying to do something I think is pretty easy. I created some ROIs in afni(that I also have > in analyze format). I would like to overlay them onto inflated and folded surfaces > produced in freesurfer. Should I treat these as functional overlays and treat it > as functional data or is there another way? > Thanks, Oleg Leontiev

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Re: Re: [Freesurfer] statistical tools in freesurfer
by Glenn Lawyer 01 Dec '04

01 Dec '04

Thanks, Bruce and Doug. That's what I needed to know. the mris_glm --help output was nice and thorough. +glenn > You can also use mri_surf2surf to convert to analyze, use other tools > (such as FSL) to do your group analysis, and then use mri_surf2surf to > convert the result back to something that can be displayed by tksurfer > (eg, a .w file). > doug On Tue, 30 Nov 2004, Bruce Fischl wrote: >> Hi Glenn, >> >> part of the output of mris_make_surfaces (in addition to the ?h.white and >> ?h.pial surfaces) is a measure of the cortical thickness, contained in the >> file ?h.thickness. You can do group analysis of these files in two ways. >> For a simple comparison of means or a t-test, you can use mris_twoclass. >> For a more sophisticated GLM analysis, you can use mris_glm. >> >> cheers, >> Bruce > -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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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-

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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.

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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 > <><><><><><><><><><><><><><><><><:)

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Freesurfer