Freesurfer December 2004

freesurfer@nmr.mgh.harvard.edu

21 participants
28 discussions

Stats and viewing parcellation problem
by Brian Schweinsburg, Ph.D. 07 Dec '04

07 Dec '04

Hi All, I am having problems computing stats using the parcellation file. In addition, when I try to display the parcellation results in tksurfer (File -> Label -> Import Annotation -> rh.aparc.annot), which were completed without an error message using parcellate_subject-rh, I get an error message. I am not sure how to procede. Any hints? In both error logs, there is a reference to an older location of the Simple_surface_labels2002.txt file, which never existed on my machine. Is that related to the problem? My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218. I appreciate any assistance. Brian ####### mris_anatomical_stats error message ####### mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 rh computing statistics for each annotation in /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno t. reading volume /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... reading input surface /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... Computing inter-vertex distance computing second fundamental form...reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 CTABreadFrom: could not allocate -1073747536 bin table Cannot allocate memory Bus error ####### Tksurfer error message ####### reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 CTABreadFrom: could not allocate -1073756992 bin table Cannot allocate memory Command Finished

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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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Freesurfer December 2004