Freesurfer July 2007

freesurfer@nmr.mgh.harvard.edu

61 participants
99 discussions

Newbie question - read error, segmentation faults and errors loading volumes-oh my
by Sheyna Gifford 17 Jul '07

17 Jul '07

Dear Freesurfer List, I have used mri_convert as per the tutorial, to great the following mgz files from dicoms: 001/mri/orig/001.mgz and 002/mri/orig/002.mgz They were created with the following call or the appropriate varient: $mri_convert -it dicom -ot mgz 002/mri/orig/002/ 002.mgz There were no major errors that appeared during the conversion, and the files that were created are valid reconstructions. I have opened them both in Neurolens and they look exactly as they should. However, when I try to tkmedit them, I get the following error: $ tkmedit 001 001.mgz mghRead(/Applications/freesurfer/subjects/001/mri/001.mgz, -1): read error Error: Loading volume 001/mri/orig/001.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. A friend suggested that I use the COR format instead of going through the mgz intermediate, which I did with the commands: $ mri_convert 002/mri/orig/002/IM-0001-0010.dcm 002 -ot cor However, I get the same error. These subjects-001 and 002-are in the default freesurfer/subjects folder. Tkmedit itself works, as I was able to run through the entire tutorial without a hitch. These are T1-weighted structural images that I am just trying to take a look at, in my first FreeSurfer foray. Not trying anything fancy, I don't think. Any help, guidance and/or suggestions would be appreciated. Sincerely, sgifford -- Sheyna Gifford Research Specialist Magnetic Resonance Imaging Research Facility Brown University Box G-L 401-863-6513

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freesurfer in cygwin
by 申林 17 Jul '07

17 Jul '07

hi, I have downloaded freesurfer in WINDOWSXP and want to run it via Cygwin. But it don't work. Is there possibility to run it ? The freesurfer I used is the public copy. I follow the "LinuxInstall" and type : tar xzvf freesurfer-Linux-rh9-stable-pub-v3.0.5-full.tar.gz export FREESURFER_HOME=<j:/cygwin/usr/local/>/freesurfer export SUBJECTS_DIR=<=<j:/>/freesurfer . ${FREESURFER_HOME}/SetUpFreeSurfer.sh and then, any command seems don't work, (e.g. mri_convert , tkmedit, tksurfer) and reture erro like this (bash: mri_convert: command not found). how to resolve the problem and how to run it normally in WINDOWSXP? thank you! Shen Lin -- Lin Shen, MMS, Department of Neurology, The First Affiliated Hospital, ChongQing Medical University No.1, Yixueyuan Road, ChongQing, 400016 China Phone: +86 23 13193076520 E-mail: shenlin918(a)gmail.com

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manual edit problem
by Kirk, Gregory 16 Jul '07

16 Jul '07

Hi, I am trying to fix the few subjects in my study ( 3 of 64 ) that need manual fixes resulting from skull strip erros ( 2 of 3 cerebelem was left out ). This is the first study since my student who was doing this for me left ... So the note he left said do tkmedit practice/subjectname/ brainmask.auto.mgz -aux orig.mgz then config brush, etc. i.e. make the edits and save changes in brainmask.auto.mgz with input from orig.mgz In the frresufer wiki tutorial it has tkmedit 091_watershed_before brainmask.mgz -aux T1.mgz i.e. make the edits and save changes brainmask.mgz with input from T1.mgz the study is with version freesurfer-v3.0 so the difference may be with version. I was unsure what to do after saving the edits, I tried copying brainmask.auto.mgz to brainmask.mgz, i.e. overwrote the file with cp. recon-all -autorecon2 -subjid <subject name> and it finished with errors. I could find no error message in the logs. I deleted the surfaces in the surface directory and reran and it again finished with errors and only 5 of the surfaces ( on the right side) had been produced. a bit mysterious since the left and right side was involved in the edits ?? anyhow see an obvious change in procedure I need to make ? thanks again Greg.

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Mean cortical thickness as nuisance variable
by Juergen Haenggi 16 Jul '07

16 Jul '07

Dear Freesurfer users We are doing an analysis on cortical thickness and we are not sure whether to include the mean cortical thickness as a covariate of no interest in our statistical model. Any suggestions are welcome. Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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add the gray matter
by Wang, Xin 13 Jul '07

13 Jul '07

Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface? Thank you in advance. Xin

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differences between mri_glmfit and intergroupavg-sess
by Robert Levy 13 Jul '07

13 Jul '07

Hello, I've comparing results of output from intergroupavg-sess with output from mri_glmfit, and the difference seems to be too huge to be accountable just from differences between the two programs. I attached images that go along with the commands below. What do you think could be the cause of these huge differences? Are there any parameters that might reduce the difference? Thanks, Rob (September 2005) intergroupavg-sess \ -group1 BwGroupNormalsError5 \ -group2 BwGroupAspError5 \ -space sph \ -spacedir sph_sm20 \ -intergroup BwGroupError5 \ -analysis EMerror \ -contrast ASevASc (Currently ran this because so I could then adjust the threshold using monte carlo data. The results of this should I think be the same or similar to the intergroupavg results) /space/greve/1/users/greve/freesurfer/bin/mri_glmfit \ --really-use-average7 \ --y rh.ASevASc_8s_BwGroupError5.fsfast.mgh \ --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ --glmdir rh.ASevASc_8s_BwGroupError5.fsfast.glmdir \ --pca \ --surf average7 rh \ --C fsgd_and_contrast_files/BwGroupError5.mat \ --label average7/label/dACC_rACC_final-rh.label \ --fwhm 4.6 -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Conversion to Minc Line OBJ
by jorge luis 13 Jul '07

13 Jul '07

Hello all I would like to convert a freesurfer triangular surface (ASCII or binary) to Minc Line OBJ file format. I know how to convert to Minc Polygons OBJ file format, but it is not useful for my application. I need a conversion to the Lines OBJ format. Any help is welcome In advance thank you very much Jorge ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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control points
by Don Hagler 13 Jul '07

13 Jul '07

In recon-all, it says you are supposed to use -autorecon2-cp if you use control points. So I wonder why earlier normalization steps also use control points, such as Norm1 and CANormalize. What effect do the control points have in those steps? _________________________________________________________________ http://newlivehotmail.com

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Problems with surfaces
by Alexander Fornito 12 Jul '07

12 Jul '07

Hi all, I'm trying to run some 3T data through freesurfer and encouter a consistent problem in the cuneus/occiptal lobes where the pial surface fails to extend the the grey/CSF boundary and instead follows the white surface. I have attached an example. This problem happens in the same area across a substantial proportion of my images. I've tried control points, but they don't seem to help. Any suggestions would be greatly appreciated. Thanks, Alex

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Image scaling in the MGZ file format
by Jerry Yeou-Wei Chen 12 Jul '07

12 Jul '07

Hello Freesurfer Forum, We have a question about the M matrix, found in the .mgz file header. We loaded an .mgz file into Matlab and took a look at the affine transform matrix M from the header: M(1,:) = [-1 0 0 132.7486]; M(2,:) = [ 0 0 1 -105.7281]; M(3,:) = [ 0 -1 0 131.7424]; M(4,:) = [ 0 0 0 1 ]; Let's call these numbers: M(1,:) = [ a 0 0 xt ]; M(2,:) = [ 0 0 c yt ]; M(3,:) = [ 0 b 0 zt ]; M(4,:) = [ 0 0 0 1 ]; We interpret a b and c as controlling rotation. xt yt zt govern translation. However, we cannot see how this matrix controls scaling. We were expecting to see the following: M(1,:) = [ xs 0 0 xt ]; M(2,:) = [ 0 ys 0 yt ]; M(3,:) = [ 0 0 zs zt ]; M(4,:) = [ 0 0 0 1 ]; ...where xs yx zs control scaling. In our empirical matrix they do not seem to be serving that function. (xs appears to be used for rotation only, ys and zs are zero). So the first question is: does the matrix control scaling, and if so, how? The second question: Is the scaling built into the image, such that each voxel is 1mm by 1mm by 1mm? If so, how can the program tell when this is the case, and when it is not? Does ndim1 represent the number of voxels in that dimension, or the distance across that dimension in millimeters? Does ras_good_flag simply indicate that the image is in the proper orientation, or does it also indicate that each voxel in the image measures 1mm x 1mm x 1mm? Thanks for your help. Jerry Chen and Geoff Pope

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Freesurfer July 2007