Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

WM mask
by Gallo, Antonio (NIH/NINDS) [F] 21 Feb '08

21 Feb '08

Dear all, We are trying to extract a cerebral white matter mask from the Freesurfer output. We are currently using the aparc+aseg file in order to do this, however we realized that the white matter mask (taken by choosing the voxels with values equal to 2 and 41) doesn't correspond exactly to the white matter we would like to have, which rather would follow the WM boundary obtained with the surface processing. Is there a way to get a more accurate mask that corresponds to these boundaries? Also, is there a description of the file format that the surface files are written in? Thank you, Antonio

3 2

Mac Pro Benchmark
by Dabbs (Kevin) 21 Feb '08

21 Feb '08

Been running Freesurfer on Linux 2.0 GHz machines. I like the results but need to increase through-put for a 500 subject run. Got the money for a Mac Pro with 8 cores and 16 GB ram. Is it likely that I will get an eight times gain in through-put? Just need some kind of benchmark to determine a reasonable schedule for this job. Thanks for any comments; Kevin Dabbs Dept. Neurology Univ. Wisconsin-Madison

2 1

qdec.table.dat & sample.levels for the tutorial data set
by Gallo, Antonio (NIH/NINDS) [F] 20 Feb '08

20 Feb '08

Hi All, I'm trying to follow the FS Tutorial for Qdec/Group Analysis, but I was not able to find the qdec.table.dat and sample.levels for the tutorial data set. Could you please help me with this? Thanks a lot, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5C203B Bethesda, MD, 20892 - USA ph #: 001-301-496.7368 fax #: 001-301-402.0373 ***********************

2 1

Obtaining cortical parcellations
by Dan Dillon 20 Feb '08

20 Feb '08

Dear FreeSurfers, I have several subjects who have fine inflated, white, and pial surfaces, as well as fine curvatures, but no cortical parcellations. Is there a directive I can pass to recon-all to generate the parcellation without having to run autorecon3 all over again? Something like "-autorecon3-parcellation"? I am running version 4.0.1. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

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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

2 3

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

1 0

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.

2 1

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

3 5

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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