Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

analyze format
by Sasha Wolosin 07 Nov '05

07 Nov '05

Dear all, When converting from analyze format is there any way to get mri_convert to read in orientation information from the analyze header file? 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.

2 2

linking tksurfer and tkmedit
by Mark Pinsk 07 Nov '05

07 Nov '05

I just finished going thru the wiki's 'recommended' workflow with one of my subjects, which is just great ! It tells me to use tkmedit to check my wm and pial surfaces after autorecon2. I did and they looked pretty good (nothing caught my eye to have to fix). However when autorecon3 completed, I could easily see a couple little defects on the spheres. 1) should i try to fix those defects and re-do autorecon3 ? I imagine so, especially if I want to cut and flatten my surfaces. 2) how do i link tksurfer and tkmedit so that I may click on the sphere and see the corresponding location on the wm volume? I can't find that explained yet in the wiki. thx! Mark ps- using the latest dev version

3 7

make_average_surface error
by Jane Aspell 07 Nov '05

07 Nov '05

Hi I have been trying to run make_average_surface but get the error below. Any idea what the problem is? Many thanks, Jane Aspell >make_average_surface --subjects jane kader anna ==================== make_average_surface ==================== input subjects: jane kader anna output subject: average mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... MRISwriteCurvature: could not open ../average/surf/lh.avg_curv No such file or directory mris_make_average_surface... reading vertex positions from orig... processing subject jane... The following must be revisited********************************** Segmentation fault PS the version info for the program i have is: ProgramName: mris_make_average_surface ProgramArguments: -all-info ProgramVersio n: $Name: $ TimeStamp: 05/11/07-11:44:07-GMT CVS: $Id: mris_make_average_surfac e.c,v 1.9 2004/01/29 14:59:12 tosa Platform: Linux PlatformVersion: 2.4.20-20.9 CompilerName: GCC CompilerVers ion: 29600 -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD

3 2

mris_anatomical_stats
by Jonathan Kaiser 05 Nov '05

05 Nov '05

I have an annotation file that covers the entire surface (each vertex has an annotation). When I run mris_anatomical_stats with the annotation file and sum the values from each annotation, I get a larger result for the surface area and a smaller value for the gray matter volume than if I run mris_anatomical_stats with just the surface (no annotation file specified on the command line). [cuneus:kentron] (nmr-dev-env) mris_anatomical_stats -a 2859_4_ct/label/rh.cmaparc.annot -b 2859_4_ct/ rh sum of each annotations' surface area: 112383 mm^2 sum of each annotations' gray matter volume: 375675 mm^3 [cuneus:kentron] (nmr-dev-env) mris_anatomical_stats 2859_4_ct/ rh total surface area = 98400 mm^2 total gray matter volume = 401366 mm^3 -Jon

2 1

spm analyzes
by Mateusz Orzechowski 04 Nov '05

04 Nov '05

Hello All, I'm totaly new in Freesurfer. Where can I find any documentation or tutorial how to make surfaces and label it using ready analyzes from spm greetings Mateusz Orzechowski

1 0

automated parcellation
by Goulven Josse 04 Nov '05

04 Nov '05

Dear Freesurfers, We have used the automated parcellation (Fischl et al, 2004) in several subjects and noticed in some cases labeling of the lateral part of a gyrus (i mean the part that's visible on the folded surface), as belonging to a sulcus. The example I have in mind is the labeling of a gyrus that could be the middle temporal or the angular gyrus as the posterior part of the superior temporal sulcus (STS). I figured the program could not find the correspondence between that particular gyrus and any labels and, since it happened to be close and, sometimes, between two branches of STS, it was labeled as such. Or we made a mistake somewhere ... ? Could anyone please comment on this ? thanks ! Goulven Josse (U of Chicago)

4 9

area file
by Marie Schaer 03 Nov '05

03 Nov '05

Hello everybody! I have one question about how surface areas are calculated by mris_anatomical stats (release2004). I noticed that the ?h.area file may contain the portion of area corresponding to each different vertex. Actually, the sum of all these areas is around 7'500mm^2 for one hemisphere, which is approximately (but not exactely) the result given by mris_anatomical_stats. However, when I converted the pial surface in matlab, and calculated the sum of the area of each triangle using the following equation http://mathworld.wolfram.com/TriangleArea.html, I obtained a very higher result (~10'000mm^2). Perhaps because the triangles are too big to calculate an accurate area at this stage? So my question was, on which basis is calculated the information contained in lh.area? Does the first row of ?h.area correspond to the piece of area attributable to the first vertice, and so on? Thank you very much for your response! Marie Schaer

4 5

freesurfer tutorial
by peggy christidis 03 Nov '05

03 Nov '05

Would you consider providing a .pdf version of the web document "FreeSurfer Tutorial: Morphometry and Reconstruction" that could be easily downloaded and printed out? We occasionally teach a FS class here at the NIH and I know it helps to have a paper-version of the manual to refer to (which is very nice by the way, well-written). Thanks! Peggy

2 1

coordinate transform functional -> COR-anatomy (fwd)
by Claus Tempelmann 03 Nov '05

03 Nov '05

Hello, on behalf of a collegue who has not yet registered for the freesurfer mailing list I want to send you the questions below. Thanks for your help Claus ----------------------------------------------------------------------- Hi, we are currently trying to spatially transform functional data into the anatomical 256*256*256 1mm isovoxel COR-anatomy. We already have a register.dat and therefore a rotation-translation matrix. Our functional data are in a 128*128*24 bshorts file (1.406*1.406*2mm voxels). Slice orientation is approximately orthogonal to the calcarine sulcus Our problem is that the functional data do not fall on the correct location in the anatomical volume. Our approach so far is: We built a datacube from the anatomical COR* files and oriented it with respect to the RAS system so that: R corresponds to -X (the inverted first coordinate direction in our data cube) A corresponds to Y S corresponds to Z >From the functional data (in bshort format) we reconstruct a similar volume and orient it the same way. We assume the origin of the two coordinate system (the anatomical and the functional) in the center voxel of the two volumes Whe now calculate [xAnat, yAnat, zAnat,1]'=[4*4-matrix from register.dat]*[xFunctional, yFunctional, zFunctional,1]' The x*, y* and z*s are in millimeters. An example: we choose the voxel in the center of gravity of the functional volume [0,0,0,1]' and multiply it at the right of the matrix in register.dat. Shouldn't this give us the location of that voxel in the anatomical volume ? Our qusestions: Can the register.dat be used to transform the functional data onto the COR-anatomy ? If yes how ? How does the coordinate system look like in both volumes especially the functional? The *.bhdr file related to the functional bshorts contains RAS-coordinates of the corners of the (first ?) slice. What is the corresponding coordinate system ? Scanner, COR-anatomy ...? We already checked the wiki-site that describes the coordinate systems and transforms but this did not solve our problem. Thank you very much for your help. PS. The 4*4 transformation matrix we are using: 1.081372e+00 5.667235e-02 0.000000e+00 8.327621e+00 3.764737e-02 -7.183544e-01 -6.946586e-01 -6.509724e+01 3.635561e-02 -6.937064e-01 7.193404e-01 -4.349084e+01 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00

2 1

freesurfer + fsl
by Peter Soros 02 Nov '05

02 Nov '05

Hi All, I have installed Freesurfer for Mac OS X (2 Oct 2005) on my system (running 10.4.2) - thanks for the OS X release! Unfortunately, fsl doesn't work after the installation of Freesurfer. This is the error message I get when I try to open the fsl GUI: Error in startup script: no suitable image found. Did find: /Applications/freesurfer/lib/tcltktixblt/lib/ libtix8.1.8.4.a: unknown fi le type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /Applications/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] ! = 0 } { package require Tix tix configure -scheme TixGray option add ..." (file "/usr/local/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/usr/local/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/usr/local/fsl/bin/fsl" line 19) FSL was installed in the recommended directory /usr/local/fsl/ and worked well before. Any help to get FSL working again is highly appreciated!! Peter

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