Freesurfer September 2006

freesurfer@nmr.mgh.harvard.edu

37 participants
45 discussions

aseg, aparc regions reference table (aka "data dictionary")?
by Graham Wideman 22 Dec '06

22 Dec '06

Folks: It would be *really* great if there was a page somewhere (or just a file) giving some info on the various measures that are captured in the aseg and aparc files. For each measure (in the table or the "comments" above the table): -- Description of what it includes -- some are obvious from the name, others not. -- Whether it's deprecated. -- Whether FS V-whatever actually produces this value, or just zero. (Very useful, and probably not too much work? Plus I'd like to adapt this info so as to pull only the non-inert rows from the data file). (Or is there some other way to determine this?) -- Some suggestions on what numbers need to be added to get popular subtotals. I've just read through the last six months of freesurfer list traffic, and I see numerous questions along these lines... and replies with some clues here and there. Also references to papers, but these don't detail the nitty gritty of what FS V-something actually does. Probably numerous users would get a lot of use out of having this info in one place. Thanks, Graham

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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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Using different image acquisitions
by Nicolas Cherbuin 29 Sep '06

29 Sep '06

Hello, Is it possible to coregister a combination of T1, T2, and Flair images to obtain better results? Also, is it possible to assess freesurfer's precision by processing separately a T1 and Flair image in the same subjects taken at the same time and comparing their measures? Thanks Nic

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llibglut.so.3 problem
by XJ Kang 29 Sep '06

29 Sep '06

Hi, I installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz <http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-centos4_x86_64-…> on my Redhat Enterprise Linux WS release 3 (64 bit). When I ran the progam tkmedit or tksurfer, the error messages are: tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory The I created links % ln -sf /usr/lib/libglut.so.3.7.0 /usr/lib64/libglut.so.3. Still, I got the same error, although I updated the lib links and even reboot the machine. Any ideas? Thanks. XJ

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Freesurfer and 64 bits Itanium processors
by Nicolas Cherbuin 29 Sep '06

29 Sep '06

Hi I need to process a large number of scans which could take me a lifetime with my current worksation. I could have access to a linux cluster of Itanium 64 bits machines. However, presently a distribution for Itanium processors does not seem to be available. Is there a possibility to have a version compiled for this platform? Thanks Nic

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roisummary question...
by Cameron Ellis 28 Sep '06

28 Sep '06

Hi, I am running an ROI analysis on a set of event-related data obtained through spmhrf analysis. When I run roisumamry-sess to obtain the values needed to calculate a percent signal change the number of estimations per condition is 1, which makes sense since I am looking at the entire time window. I have three conditions, however, and only three numbers corresponding to each condition to be used in a total % signal change calculation are generated. My question is, how are these overall values for each condition calculated? More specifically, how are the TRs assigned to a particular condition to calculate a value specifc to a condition when each condition overlaps within the timewindow? Thanks in advance to anyone who can help, Cameron

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breaking up dti data set
by Dennis Jen 27 Sep '06

27 Sep '06

Hi, I have a DTI dataset of size 128 x 128 x 60 x 9. I'd like to convert it into 9 volumes of size 128 x 128 x 60. Is there a utility I can use for this? Thanks, Dennis

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suse 10.1 / CentOS 4 v3.0.3 / tksurfer Problems
by Lei.Zhang＠uniklinik-freiburg.de 27 Sep '06

27 Sep '06

Hi, Dear FreeSurfers, I am running freesurfer (centos 4 / v3.0.3 under SuSE 10.1). I got the following Error while trying to run surf-sess: surfer: ### GL window already open: can't open second % freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glitInit'. I found the same problems in the mailing list which is http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03266.html , but I’m sorry that I can’t use the new tksurfer on ftp://surfer.nmr.mgh.harvard.edu/pub/dist because that is special for an x86_64 system. Please help me and thanks in advance! Lei Zhang

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Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

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tksurfer time course script help
by raij＠nmr.mgh.harvard.edu 26 Sep '06

26 Sep '06

Dear Freesurfers, We are trying to write a tksurfer tcl script that would save FIR analysis hemodynamic waveform time course windows in postscript format (rgb or tiff are not sufficient as we need to do a lot of editing on the figures with Adobe Illustrator to get publishable figures. No, not THAT kind of editing :)). The script loads a label, loads a hemodynamic waveform, calculates the mean value across the label, and plots the curves. Most of the stuff is working already, thanks to Kevin Teich, but a few pieces are missing. The functions we are looking for exist in the GUI, but we could not find the corresponding script commands in the wiki or archive. Could you tell us the tcl script commands for: 1. Save the time course window in /<path>/<filename-timecourse>.ps 2. Select only some of the contrasts for display (e.g., we have contrasts 0-7 and only want to display 1, 2, and 3) 3. Setting "subtract pre-stim average" on, i.e. forcing the pre-stimulus time window mean values to zero on the y-axis ("baseline correction"). I will add the script to the wiki when we have it working. Very convenient when you have multiple contrasts in multiple experimental conditions and many ROIs in many subjects - just edit the list of ROIs/labels and time courses to be loaded, and let the computer do the rest! 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 U.S.A. raij(a)nmr.mgh.harvard.edu

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Freesurfer September 2006