Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

strange segmented image data
by Frederick Klauschen 21 Sep '06

21 Sep '06

Hi, when loading the segmentated data into Matlab I get an image containing four smaller subimages (see attachment) instead of one (fullsize) that corresponds to the original input dataset. Does anybody know what went wrong? Frederick __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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regdat2xfm problem
by Stefano Pellegrini 20 Sep '06

20 Sep '06

Hi everybody, I have a problem with regdat2xfm. I have a reg.dat file that I made using tkregister2 to register a couple of volumes (targ .mgz and mov .img) from one of my subjects. Now, if I try to use the reg.dat file with tkregister2 and the two original files, everything is fine: I ask tkregister2 to read the reg file and the registration is what I made before. Then I convert reg.dat in reg.xfm, and I want to use the .xfm file with mincresample (after having converted the mov .img file in a .mnc file with mri_convert), I get a completely wrong transformation. also, I was wondering if there is anyway to write the output transformed volume directly inside tkregister2. these are the commands I am using data: targ.mgz mov.img (the file I want to move onto targ.mgz) commands: tkregister2 --targ targ.mgz --mov mov.img --regheaders --reg reg.dat regdat2xfm WM.img targ.mgz reg.dat reg.xfm mri_convert targ.mgz targ.mnc mri_convert WM.img WM.mnc mincresample -transformation reg.xfm -like targ.mnc WM.mnc reg_WM.mnc thanks, -stefano

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Coordinate system clarification please
by Graham Wideman 20 Sep '06

20 Sep '06

Folks: I am (still!) trying to get traction on some aspects of the current FS coordinate system(s). In the recon-all pipeline, am I right in assuming that from orig.mgz all the way through to aseg.mgz and then on to brain.mgz, wm.mgz and so on, that there's NO resampling to a new coordinate system (eg: the specific brain's data doesn't get resampled to rotate or talairach it)? Ie: if you overlay, for example, wm.mgz's data onto orig.mgz, it'll align properly? (Ie: overlay the raw voxel data, unmolested by any clever viewer transforms...) I *think* I'm right on this, but it's hard to be sure, because for example, mri_ca_normalize's docs say that it takes a gca transform file as input. But that *might* be so that mri_ca_normalize can resample some other standard file to match the specific brainmask.mgz file. <scratching of head> Graham

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Quadrangle surface formats
by Graham Wideman 18 Sep '06

18 Sep '06

Probably for Nick or Bruce? Is it the case that the quadrangle surface formats are obsolete, and only the triangle surface is currently used? Thanks, Graham

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FW: field sign and colour lables
by kristofer kinsey 16 Sep '06

16 Sep '06

I have a question regarding colour labelling for the retinotopic maps generated by Freesurfer. I'm running Freesurfer-Linux-rh9-stable-pub-v3.0.2 and have successfully generated the polar, eccen, and field sign maps (no errors). The images seem to differentiate the occipital regions, except that the colour labelling appears to be incorrect. In the eccen image, for example, the order of the colours start out as red, green, blue and using the Configure Overlay Display Inverse it's green, blue, red. According to my notes one should see fovea=red, parafoveal=blue and periphery=green. Also, with the field sign image, the area that should be V1 shows up as blue instead of yellow (can't seem to invert the colours). I've since gone back to double check that my procedure is correct and re-checked my registration and can't seem to find my mistake. I was hoping to get some help to fix this problem. In case it helps, I've attached a few images of the maps that were generated. Cheers kk ______________________________ Kristofer Kinsey, PhD Neurosciences Research Institute School of Life and Health Sciences Aston University Birmingham B4 7ET Web Site: www.physiol.ox.ac.uk/~kk3/

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tksurfer marking nodes on "opposite" side of brain
by Johannes Klein 15 Sep '06

15 Sep '06

Hi everyone, I'm currently hand-drawing some labels using tksurfer. Unfortunately, quite often a node that I try to click will not be selected. Instead, the mark is placed on the surface "behind" the one I'm viewing, e.g. when trying to outline calcarine structures, the node mark will appear somewhere on the lateral surface. I wonder if anyone else has run into this? Is it possible to constrain tksurfer's node selection to the currently visible part of the cortex only? Alternatively, an undo feature to de-select the last point clicked would save me re-drawing the whole outline, but in my Edit menu, tksurfer consistently says "Nothing to Undo". Do I need to enalbe the Undo feature somewhere? I'm running FS 3.0.3 centos4. Thank you very much, Johannes

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resampling spm2 activations
by Kirk, Gregory 14 Sep '06

14 Sep '06

Hi, I think this is one for Doug, Thomas Witzel told me it is possible to resample the volume activation data from spm2 onto the cortical surface generated with freesurfer. Is their a blurb around that details the process or could you give me some instructions. thanks Greg.

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dicom to 4d nifti
by Aapo Nummenmaa 14 Sep '06

14 Sep '06

Hi, Referring to the mail-archive: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03460.html it is now possible to convert directly from dicom to 4d nifti in the dev-version of mri_convert, if i understand it correctly. Can one get the new version of mri_convert from somewhere for testing? Thanks, -Aapo

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Group analysis of curvature not running
by Per Alm 14 Sep '06

14 Sep '06

Hi, I have been running group analysis of thickness, with no problems. However, when trying to run a group analysis of curv.pial the mri_glmfit crashes. I'm basically using the same group descriptor file, contrast matrix, and command line as for thickness, but keep getting the error message: Matrix condition is 1 search space = 104352 ERROR: dimension mismatch between y and X. y has 1 inputs, X has 31 rows. I'm running a very simple analysis, with just two groups, 31 subjects, and no variables. Ideas? Thanks, Per

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Red Hat Linux Enterprise
by Juergen Haenggi 14 Sep '06

14 Sep '06

Dear FreeSurfer user which FreeSurfer version I have to use when running OS Red Hat Linux Enterprise? Red Hat Linux 9 or CentOS 4? Because there are many mails in the FreeSurfer archive that pose questions with respect to Red Hat Linux Enterprise, I concluded that FreeSurfer runs also on Red Hat Linux Enterprise! Right? Thanks in advance for helping Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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