Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

20 Feb '08

Hi, I have siemens mrs data which are exportet as raw data at the scanner. I haven't still a possibility to convert it to dicom. But the header entries looks similar to dicom. It contains Size entries and normal vectors: ################ SliceThickness: 25.000000 PositionVector[0]: -140.282130 PositionVector[1]: -190.229627 PositionVector[2]: -149.289767 RowVector[0]: 0.990890 RowVector[1]: 0.030539 RowVector[2]: 0.131169 ColumnVector[0]: -0.017296 ColumnVector[1]: 0.994742 ColumnVector[2]: -0.100938 VOIPositionSag: -7.599275 VOIPositionCor: -26.662493 VOIPositionTra: -46.134291 VOIThickness: 80.000000 VOIPhaseFOV: 300.000000 VOIReadoutVOV: 300.000000 VOINormalSag: -0.133562 VOINormalCor: 0.097749 VOINormalTra: 0.986208 VOIRotationInPlane: -0.017453 FoVHeight: 300.000000 FoVWidth: 300.000000 FoV3D: 200.000000 PercentOfRectFoV: 1.000000 NumberOfRows: 16 NumberOfColumns: 16 NumberOf3DParts: 8 PixelSpacingRow: 18.750000 PixelSpacingCol: 18.750000 PixelSpacing3D: 25.000000 ########################### I want register other modalities to this file. So I need the fsl registration matrix. I think there are several ways to do this: - calculate manualy the qform and put it in a fake-nifi to do a registration with tkregister over the header info - make a fake dicom with the entries form the rda, try the same My question: Is there a better more direct solution without a fake file? Like giving tkregister or a other tool the cosines and other information from the header of the raw data and a second nifti file to obtain the fsl registration matrix? Best regards, Jörg -- Jörg Magerkurth Diplom-Physiker Klinikum der Johann Wolfgang Goethe Universität Institut für Neuroradiologie Schleusenweg 2-16 (Haus 95) 60528 Frankfurt Tel: (++49)(+69)6301-83822 Fax: (++49)(+69)6301-7176 www.bic.uni-frankfurt.de

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qdec vertex selection
by James N. Porter 20 Feb '08

20 Feb '08

Howdy- I am working in qdec and having a problem selecting vertices. I can move the cross-hairs by entering a vertex number in the "Jump to vertex number" box, but I can't actually just click on the brain to get the vertex where I want it. Also, the ctrl-click function to pull up the scatterplots does not work. I can imagine that there could be a translation problem of the click signal within my VNC program, but I have found no other functions, even within qdec, that do not respond to my clicking. Any troubleshooting suggestions? -- --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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checking accuracy of talairach_with_skull.lta transform
by Michael Harms 19 Feb '08

19 Feb '08

Hello, In your experience, is the "talairach_with_skull.lta" transform always reasonable, or does it sometimes fail (and if the latter, is the failure rate dependent on the FS version, as is the case for talairach.xfm ?) I ask because the ICV ("eTIV") value is derived from the determinant of "talairach_with_skull.lta". So, if we want to use the eTIV values as a covariate, should we be verifying the accuracy of this transform? And if so, what would the syntax be to do this in tkregister2 ? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Extracting brain region with a mask
by Anil Roy 19 Feb '08

19 Feb '08

Hello All, I used mri_binarize to create stg masks (inclusive of gray and white matter). I'm trying to take this a step forward to see if I can extract the actual brain region encompassed by the mask - in other words, is there a way to cut out the portion of the brain that the mask encloses. So instead of this being a binary mask with stg =1 and everything else 0, could we get everything else to be 0 and stg to remain as it is. The main reason I want to do this is that I have some other software that can create intensity histograms for such extracted regions and also perform some other analysis. Thanks, Anil.

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creating a custom overlay
by Catherine Hartley 19 Feb '08

19 Feb '08

Hi, I'm wondering whether it is possible to create an overlay consisting of a subset of clusters from a sig.mgh file, filtered according to custom criteria and preserving the significance value of each vertex in the remaining clusters so that the overlay can be thresholded as I choose. For example, if I wanted to remove a selected set of ten clusters from a sig.mgh file to yield a new one, is there an easy way to do this? Thanks, Cate

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How to see the effect of external regressors?
by Zhen Zonglei 19 Feb '08

19 Feb '08

Dear FS and fsfast expert: We want to know the effect of some external regressors such as the reaction time of every trial. We found that external regressor can be integrated into the GLM model with mkanalysis-sess's 'extreg' option, but we did not find the way to do comparison of these external regressors and see the effects of them.Do you know how to do it with fsfast? Thanks in advance for any help! Zonglei Zhen

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mri_label2vol
by bell0368＠umn.edu 19 Feb '08

19 Feb '08

Freesurfers, I wish to use a concatenated .mat file created using FSL tools within the mri_label2vol tool. Is this possible? Is it possible to convert a .mat file to a register.dat file, which seems to be the format that mri_label2vol expects? Also, what interpolation method does mri_label2vol use, out of curiousity. Chris Bell

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Problem make_average_subject
by Juergen Haenggi 19 Feb '08

19 Feb '08

Dear FS experts I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error: [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% I set the descriptor limit to 4096, but the make_average_subject command will not start anymore. Any idea what is wrong here? 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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'.license' file
by Henrique Fernandes 19 Feb '08

19 Feb '08

The installation was successful! I have created the file in 'pico', as Nick Schmansky told me to do, and fortunately the file '.license' was successfully created. Thank you all for your kind attention, Regards, Henrique Fernandes

1 0

".license" file
by Henrique Fernandes 19 Feb '08

19 Feb '08

Thanks for the suggestions, I'm now having another problem. I created a .license file with the information about my license. Although, to keep the file stored I must have a name for it other else the system won't allow me to create that file. So, after giving a random name to the file, during the test for installation I received an error message like the one above: -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- How should I create the file .license? Any suggestions? Thanks in advance fot he help, Regards Henrique Fernandes

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