Freesurfer November 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
59 discussions

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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Re: Installation Question
by DG MCLAREN 13 Nov '06

13 Nov '06

Whom should I contact with installation questions? Specifically: I am running RHEL 3 and tried to install CentOS4, which was recommended for RHEL 4. However, the libglut.so.3 library can't be found. Is there an older version of Freesurfer that would run on RHEL 3 or can that library be installed? Any thoughts would be appreciated. Best Regards, Donald McLaren ===================== D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Tel: (773) 406 2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406 2464 or email. ----- Original Message ----- From: freesurfer-owner(a)nmr.mgh.harvard.edu Date: Friday, November 10, 2006 3:43 pm Subject: Installation Question To: dmclaren(a)wisc.edu > You are not allowed to post to this mailing list, and your message has > been automatically rejected. If you think that your messages are > being rejected in error, contact the mailing list owner at > freesurfer-owner(a)nmr.mgh.harvard.edu. > >

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surface based cortical volume estimates
by Paul Greenberg 09 Nov '06

09 Nov '06

Hello, When viewing cortical surfaces and labeled volumes (aseg) with TK medit, the cortical surface runs through about 1/2 of the hippocampal volume in each hemisphere. Will this partial hippocampal volume be included in any of the surface based estimates of cortical volume found in the [?h.aparc.stats] file? Thanks very much! Paul

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white matter segmentation
by Jenny Kirchner 09 Nov '06

09 Nov '06

Hi, I am working on a case for which I have run autorecon 2. Edits seem necessary on both the pial surface and the white matter segmentation. I am now wondering if it is better to first do the white matter edits and then run autorecon 2 again to see if the pial surface errors improved or if it is more economic to do the pial surface edits in the same step. I also have a question concerning the differences in segmentation between the wm.mgz and the ?h.white. I am attaching two screenshots for you to be able to see it. The wm.mgz is showing white matter, which in the lh.white (loaded on top of the brainmask.mgz) is not defined as white matter as shown by the yellow line. (See temporal pole of the left hemisphere). I am wondering which of the both segmentations is correct, the wm.mgz version or the lh.white version and where exactely I have to do the edits. Thanks a lot for your help! Best, Jenny

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editing pre-existing annotations
by Eric Feczko 09 Nov '06

09 Nov '06

Hey, Is there a way to add structures/labels to a pre-existing annotation file? I sampled an annotated atlas onto a subjects surface. But when I load the annotation and try to create a new label, I can't export the edited annotation without eliminating the new label. I tried to create a new color lookup table with the new structure included, and I can load the table in tksurfer just fine. However, when I also try to import the pre-existing annotation(in order to edit it), the color table existing in the annotation overrides the color lookup table I load. If it try to load the table after importing the annotation, the new structure/label does not show up in the label window. If anyone can help me with this issue, that would be great, thanks! -Eric

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Addendum: Surface-Based Group Analysis Results --> MNI coordinate space
by emoulton＠mclean.harvard.edu 08 Nov '06

08 Nov '06

Had made a slight error in my previous request. Here it is, clarified: Is there a straightforward way to convert Surface-based Group Analysis results (e.g. sig.mgh) to ANALYZE format in conventional MNI coordinate space (i.e. viewable with FSL)? What steps, and what tools, should I use to perform such a conversion? Thanks, Eric 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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Surface-Based Group Analysis Results --> Original coordinate space
by emoulton＠mclean.harvard.edu 08 Nov '06

08 Nov '06

Hello, Is there a straightforward way to convert Surface-based Group Analysis results (e.g. sig.mgh) to ANALYZE format in conventional coordinate space (i.e. viewable with FSL)? It seems to require a bit more gymnastics than a simple mri_convert command to properly convert these surface maps. What steps, and what tools, should I use to perform such a conversion? Thanks, Eric 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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Freesurfer November 2006