Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

nu_correct error
by oxro03＠yahoo.com 22 Feb '08

22 Feb '08

Hi, I am trying to run an MPRRAGE scan through the first step of autorecon-all, but get the following error message: Iteration 1 Thu Feb 21 14:57:06 PST 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.28541/nu0.mnc ./tmp.mri_nu_correct.mni.28541/nu1.mnc spawn: exec of nu_estimate_np_and_em failed: No such file or directory nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct I have attached the recon-all log file. Does anyone have an idea why this happens? I get the same error from other scans from the same source. Thanks a lot, Thomas --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

2 1

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

2 1

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 --------------------------------------------------------------------

3 5

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

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Freesurfer