Freesurfer June 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
107 discussions

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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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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Intel Mac
by Ray Fix 19 Aug '06

19 Aug '06

Hello, Any plans for a Mac OS X Tiger Intel release? Ray

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Spherical morphometry
by Chacko Cherian 13 Jul '06

13 Jul '06

Hello everyone, In spherical morphometry,to create the spherical surfaces,Im using the step 8.1 in the Wiki tutorial. Could someone please explain what the colors stand for? DOING "tksurfer subj001 rh sphere" gives me a sphere on the display.But I'm not able to map it and provide the overlay info rh.curv. the command "tksurfer -subjid subj001 -morph" gives me the error "Flag unrecognized".. THanks in advance. Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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File Conversion Inquiry
by Gregory Scott 03 Jul '06

03 Jul '06

We have complex-valued volumes (retinotopic mapping data) in structural space (1,1,1mm) We'd like to convert this to a surface overlay (.w) Can mri_vol2surf handle complex data and can Freesurfer display this? (with some sort of color wheel scheme) Also, does freesurfer require both polar and eccentricity mapping data simulateously or can one display (eg. polar mapping) data separately? Thank you very much for your time and any help Sincerely, Gregory Scott

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tksurfer/suse 10.1 troubles
by Sebastian Moeller 02 Jul '06

02 Jul '06

Hi List, running freesurfer (centos 4 x86_64 3.0.2 pub full under SuSE 10.1 (had to upgrade from 9.3 because of stability issues)) I get the following Error while trying to run surf-sess (over ssh tunneled X11): surfer: ### GL window already open: can't open second % freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glitInit'. Interestingly both SuSE 9.3 and 10.1 use libglut.so.3.8.0 (freeglut). The exact command I ran from the mystudy directory is: surf-sess -sf sf -df df -analysis a3 -contrast c1_2 -hemi lh -surf inflated This exact command worked with SuSE 9.3 (all OSs 64bit linux). I am downloading 3.0.3 ATM to see whether this was fixed. If any of you have any advise I am keen to hear it ;). Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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mri_segstats only generated values for index 0-82
by Nguyen, Thang Q 30 Jun '06

30 Jun '06

Hello all, I was able to generate statistics on functional overlays but for some reason, the statistics do not have values after the structure name "Right-non-WM-hypointensities." Everything after this region listed has values of zero for the Mean, StdDev, Min, Max, and Range. The command I used is listed below: mri_segstats --brain-vol-from-seg --in subbj1.img --seg aseg-in-subj1.img --ctab-default --sum -subj1.output.txt Is this a problem with the registration, the command line, or something else? Thank you for your help, -Thang Nguyen

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Aseg.stats measurements
by Goradia, Dhruman D 30 Jun '06

30 Jun '06

Hi all, Can anyone tell me how freesurfer defines Intracranial volume, Brain segmentation volume and Brain mask volume? What is the difference between the 3 measures? -Dhruman

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help: freesurfer on debian amd64 (problem with libtiff)
by Davide Anchisi 30 Jun '06

30 Jun '06

Hi, I have an amd64 machine with a Debian GNU/Linux (v. testing) system. I'd like to use freeSurfer but I got some problem. I installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz When I run tkmedit (or tksurf) I get the following message: tkmedit: error while loading shared libraries: libtiff.so.3: cannot open shared obj ect file: No such file or directory On my system I have libtiff4. Any suggestion? Thanks, Davide

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surface area
by Sasha Wolosin 29 Jun '06

29 Jun '06

Dear all, Are the regional surface areas computed by mris_anatomical_stats using the ?h.white surface or the ?h.pial surface? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Freesurfer June 2006