Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30066 discussions

visualizing ASL images
by Abi Gopal 17 Nov '06

17 Nov '06

Hello all I'm new to the freesurfer mailing list, so I was hoping I could get some advice here. As part of my research, I have been acquiring arterial spin-labeling (ASL) images of subjects with cortical dysplasia (a type of brain malformation). However, I've been having problems visualizing the ASL images individually. Specifically, when I extract the ASL images in .DCM form, all 12 of them show up on a single picture. Do you know of any way to extract them individually, so that I can view a single slice on each page? I really appreciate any help you can give me. Thanks Abi -- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School

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edit wm or pial?
by Reschke, Cole 16 Nov '06

16 Nov '06

Looking near the center of the picture, you will notice that the pial surface crosses the white matter. This is one of two slices where this happens. Is this a case where I edit the pial surface or the white matter, or both? Cole Reschke Data Manager, PET Center Banner Alzheimer Institute Banner Good Samaritan Medical Center Phone: (602) 239-4868

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annotation2label problem
by Cameron Ellis 16 Nov '06

16 Nov '06

Hi Everyone, When running mri_annotation2label for an individual subject one label is not extracted. The processing text says: 0 empty skipping. Does anyone know why this is happening and if I can get this label extracted? Do I need to re-run part of the autorecon process? Thanks, Cameron

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sig.mgh = -log(p)?
by Eric Moulton 16 Nov '06

16 Nov '06

The -log 10(p) image contains negative values, and when we convert these these values into p-values, we get p-values greater than 1. Is there possibly something wrong with the image? The sig.mgh histogram looks like a t-distribution (viewing with tksurfer...Configure Overlay Display...also after converting to ANALYZE format as viewed by fslview:Image Histogram). Thanks, Eric Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772 Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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Re: [Freesurfer] mri_convert and GE dicom
by Doug Greve 15 Nov '06

15 Nov '06

So, to be perfectly clear, the problem is *not* with the FreeSurfer tools. The problem is with fslview. While it reads the orientation information, it does not act upon it in order to reorient the images in a reasonable way. FSL has rather strict requirements on how the pixels must be arranged in order to use the tools (see www.fmrib.ox.ac.uk/fslfaq) -- this is above and beyond simple left-right orientation. Interleaved axial images from a Siemens scanner will, by default, not be arranged correctly. FSL provides tools to flip and reorient the data (this cannot be done with mri_convert). Try viewing the volumes in tkmedit (which is geometry-aware). If tkmedit displays them incorrectly, I will happily fix the problem. doug On Wed, 15 Nov 2006, David M Schnyer wrote: > Well, good point. When I bring it into FSLview the brain is not oriented as > expected. For example the lower left window has axial scans that are upside > down. Interestingly, the labels show the correct directions since A is > pointing down and P is pointing up but I have run into trouble in the past > running images like this through the FSL stream. Anyway, I will put these > images somewhere local where you can get at them when I get in tomorrow. > thanks, > > david > > Doug Greve wrote: > >> >> How do you know it's the wrong orientation? Is the data local to the >> our network? >> >> >> >> >> >> On Wed, 15 Nov 2006, David M Schnyer wrote: >> >>> I have been trying out the dev version of mri_convert on some GE dicom >>> images. This is functional data. If I leave the orientation alone and just >>> convert from Dicom to nifti then I get a timeseries volume in the wrong >>> orientation. OK, so I add the flag --out_orientation RAS. Here I get a >>> volume in the right orientation but the timeseries is gone. Now, it isn't >>> really gone, in that the file is the correct size but FSL no longer sees >>> it as a timeseries. Anyone dealt with something like this? >>> >>> thanks, >>> >>> david >>> >>> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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mri_convert and GE dicom
by David M Schnyer 15 Nov '06

15 Nov '06

I have been trying out the dev version of mri_convert on some GE dicom images. This is functional data. If I leave the orientation alone and just convert from Dicom to nifti then I get a timeseries volume in the wrong orientation. OK, so I add the flag --out_orientation RAS. Here I get a volume in the right orientation but the timeseries is gone. Now, it isn't really gone, in that the file is the correct size but FSL no longer sees it as a timeseries. Anyone dealt with something like this? thanks, david -- David Schnyer, Ph.D. Imaging Research Center & Department of Psychology University of Texas, Austin tel: (512) 471-8505 fax: (512) 232-4202 http://irc.utexas.edu/index.html

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mri_convert SC dicom
by Kirk, Gregory 14 Nov '06

14 Nov '06

Hi folks, I was trying to convert an dicom MPRAGE with a SISCOM activation( grayscale ) to nii format to use the activation for a seed for probalistic fiber tracking. The siscom is created in Analyze(program not file format) and then exported to dicom , so it is a secondary capture siscom. I know this is not really a freesurfer thing but I guess you guys when possible try to make your tools mutually usefull so I send the error in case you see a simple fix by an option I can apply. set orientation seems to be the issue notice k_ras = (nan, nan, nan) also WARNING: NumberOfFrames 0 != Found Count of slices 104. thanks if you can help Greg. reading from i170927.SCPT.1... 104 DICOM 3.0 files in list Found 104 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 104. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /home/gkirk/tillsis/dicom/i170927.SCPT.1 Date and time study date 20061114 study time 142154 series time 142014.000000 acquisition time 142014.000000 Identification patient name manufacturer SIEMENS NM Dimensions number of rows 256 number of columns 256 number of frames 104 pixel width 1 pixel height 1 slice thickness 2 field of view 256 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 4.7 repetition time 1870 inversion time 1100 echo number 0 flip angle 0.261799 bits allocated 8 Spatial information first image position -132.963 -132.808 -122.125 last image position -132.963 -132.808 -122.125 image orientation 1 -2.05103e-10 0 2.05103e-10 1 0 ------------------------------------------------- TR=1870.00, TE=4.70, TI=1100.00, flip angle=15.00 i_ras = (-1, 2.05103e-10, 0) j_ras = (-2.05103e-10, -1, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): source matrix has zero determinant; matrix is: -1.000 -0.000 nan nan; 0.000 -1.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; [gkirk@Nuit dicom]$

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help with cortical thickness maps
by Abi Gopal 14 Nov '06

14 Nov '06

Hello all I have a basic question. How do I create cortical thickness maps? I have been through most of the freesurfer tutorial and understand most of the commands. However, I am wondering how I can create a cortical thickness map for some of my own MRI data. Please let me know what steps I should take to do this. Thanks! Abi -- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School

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tksurfer BOLD time course display: show multiple overlays?
by raij＠nmr.mgh.harvard.edu 13 Nov '06

13 Nov '06

Hi Surfers, To facilitate comparison of ROI BOLD waveforms across different experiments we are trying to find a way to plot time courses of *** multiple overlays *** simultaneously in the tksurfer time course window. Is there a way to do this using the tcl script? Usually the time course window shows the multiple contrasts for a single overlay, but as soon as I change the overlay, the old time courses are erased and the time courses change to the new overlay. I guess what I am saying is that we would like to avoid erasing the old stuff in the time course window and just keep adding more waveforms from new overlays (with the possibility of still selecting which waveforms will be visible). We are trying to do this within tksurfer. Any suggestions are much appreciated! Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 USA

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problem interfacing freesurfer with AFNI/SUMA
by Anthony Steven Dick 13 Nov '06

13 Nov '06

Hello all- We have encountered a problem interfacing Freesurfer with AFNI/SUMA. The problem occurs specifically with the creation of standard meshes (using the MapIcosahedron program in SUMA)--they come out very distorted. This occurs even though the individual's surface looks pretty good. We have talked to the people at AFNI, and they have told us that our surfaces from Freesurfer are the problem, and that we need to do some manual editing. We think our surfaces are pretty good. Additionally, we have never encountered this problem in the 3 years we have been using Freesurfer and interfacing with AFNI. The problem began when we downloaded and used Freesurfer 3.0.1. Of course it could be our surfaces require more manual edits, and we are looking into that. However, I wanted to post to find out if: a) Anyone else is encountering this problem, especially recently b) Does anyone have any other ideas about why it would just be appearing now? We know it was not a problem in the past. Additionally, we have recently tried a very old freesurfed brain (over 2 years old), and it comes out pretty good. Any ideas? Thanks. Anthony -- Anthony Steven Dick, Ph.D. Post-Doctoral Scholar Human Neuroscience Laboratory Biological Sciences Division University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: adick(a)uchicago.edu Alternate email: anthony(a)anthonymail.com Please visit my homepage at http://home.uchicago.edu/~adick/

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