Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

mris_thickness_diff computation method?
by David Perlman 09 May '07

09 May '07

In the documentation of mris_thickness_diff it says "This program computes the difference of two surface data sets defined on the two surface mesh. Result = data2 - data1 (in sense of closest vertex)." Also, on the thickness repeatability page, it states that the output of mris_thickness_diff is sampled on the first surface. Just want to make sure I'm understanding this correctly: this means that mris_thickness_diff does NOT resample the data onto a common mesh to do vertex-wise subtraction, but rather, for each vertex in surface1, it finds the spatially closest vertex in surface2 and then subtracts the data2 at that point from data1 at the original point. So I assume this means that using mris_thickness_diff, even if you have two thickness data files which are sampled on the *same* mesh, if they are physically not aligned in space for whatever reason, you will get very wrong results? (I think I had this problem earlier and didn't understand what was going on.) One more question about the thickness repeatability page. How will the results obtained in this way differ from results obtained by aligning the surfaces with mri_surf2surf and simply doing a vertex- wise subtraction using matlab? -- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe

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fMRI stats on the surface
by oxro03＠yahoo.com 09 May '07

09 May '07

Hi Doug & Ohers, I see that there are nice interfaces between Feat and Freesurfer for rendering Feat output onto the surface. Now for group fMRI stats it would obviously be advantageous to do all the stats directly on the surface, avoiding volume space altogether. Especially clsuter thresholding might be an issue here. Am I correct there? What approach would you suggest in terms of what software to use for the fMRI analysis. In our lab we have used mainly FSL tools to do volumetric fMRI analysis, and are hence most familiar with these, but are considering to moving to doing all this on the surface. What are people's views on that? Is that an entirely good thing or are there advantages to volume space analysis? What if spatial distortions are present in the BOLD images and haven't been corrected for? Any comments and suggestions on these issues would be greatly appreciated. Thanks a lot, Christine --------------------------------- Looking for earth-friendly autos? Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center.

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Make_average_subject error
by Furlong, Carolyn 09 May '07

09 May '07

Hi all, I tried running it again with --no-symlink but this error came up ERROR: Flag --no-symlink unrecognized. any advice? Best wishes Carolyn

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Make_average_subject error
by Furlong, Carolyn 09 May '07

09 May '07

Hi all I have run the script make_average_subject and the error message at the end is: ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not permitted only rh* files have been created. Can you help? Best wishes Carolyn

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recon_all -long
by David Perlman 08 May '07

08 May '07

I wonder if I've reached my new-user quota of questions yet? My brand-new installation of Freesurfer doesn't seem to have the - long option available on recon-all described in Xiao Han's page on the wiki. Is this referring to a beta version of recon-all? thanks... -- -dave---------------------------------------------------------------- After all, it is not *that* inexpressible. -H.H. The Dalai Lama

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error make_average_subject
by Anthony Dick 08 May '07

08 May '07

Hi all- In attempting to use make_average_subject I encountered a problem. The process died during >mris_curvature >averaging curvature patterns 10 times. >total integrated curvature = 106.607*4pi (1339.664) --> -106 handles >ICI = 265.0, FI = 2956.1, variation=44197.937 >writing Gaussian curvature to ./rh.white_avg.K...done. >writing mean curvature to ./rh.white_avg.H...done. >reading group avg surface area 1032 cm^2 from file and ended with this error. >ln: rh.sphere: Operation not supported Any ideas? Thanks. -- Anthony Steven Dick, Ph.D. Post-Doctoral Scholar Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: adick(a)uchicago.edu Web: http://home.uchicago.edu/~adick/

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(no subject)
by hankee 08 May '07

08 May '07

Hi, In the ?h.aparc.stats file,I want to use the average thickness directly to do the statistics analysis? Can I do like that? Thank you. hankee，duhanjian(a)sohu.com 2007-05-05

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parameter settings
by Frederick Klauschen 08 May '07

08 May '07

Hi, I would like to ask if the following procedure is recommended when using FreeSurfer for (total) gray and white matter volumetry, or if specific parameter settings are known to optimize this task. "Default processing stream (recon-all -all) is used. Data are visually inspected, and manual interventions are performed where automated steps fail. These include manual alignment to the talairach template in cases where automated registration is poor, and adjustments to the watershed threshold to restore areas of the brain that are erroneously removed during skull stripping." Thanks, Frederick ____________________________________________________________________________________ Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front

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vertex normals
by burak ozkalayci 08 May '07

08 May '07

Hi all, I want to get an ascii file listing the normal vectors of each vertex of the surface (white or pial). In http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02210.html mri_surf2surf is adviced to used but I could not find any example usage for creating vertex normals. And I appreciate any help on converting the output of the mri_surf2surf to ascii file. One more question about the vertex normals. using tksurfer to see the surfaces, the normals of the selected vertices are printed on the console. to use mri_surf2surf the sphere.reg files are needed and they are created at the 3rd step of reconall. If there is any straightway to get those vertex normals from the surface definition like tksurfer do, I prefer it since I do not want to wait for the reconall 3. Thanks in advance. Burak

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mri_surf2surf resampling does not give same number of nodes
by David Perlman 08 May '07

08 May '07

I think I must be misunderstanding something about the way mri_surf2surf works. I thought it was supposed to resample onto the target mesh, which I would think would mean that resampling two different data files onto the same target mesh would give outputs with the same numbers of nodes. But when I do this and then read the resampled data into Matlab, the nodes do not match up. Here are the commands I used: mri_surf2surf --srcsubject sp01t7 --hemi lh --srcsurfval thickness -- src_type curv --trgsubject sp01MULTt1 --trgsurfval ../../sp01MULTt1/ surf/t7tot1-lh.thickness.w --trg_type w mri_surf2surf --srcsubject sp01t6 --hemi lh --srcsurfval thickness -- src_type curv --trgsubject sp01MULTt1 --trgsurfval ../../sp01MULTt1/ surf/t6tot1-lh.thickness.w --trg_type w And here's what I see in Matlab: >> [vt6to1,ft6to1]=read_wfile('t6tot1-lh.thickness.w'); >> [vt7to1,ft7to1]=read_wfile('t7tot1-lh.thickness.w'); >> size(vt6to1) ans = 124463 1 >> size(vt7to1) ans = 124134 1 What am I missing here? -- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe

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