Freesurfer May 2007

freesurfer@nmr.mgh.harvard.edu

53 participants
97 discussions

converting .xfm to register.dat
by s032441＠student.dtu.dk 10 May '07

10 May '07

Dear All Im trying to make a register.dat file by using tkregister2 --mov func.mnc --xfm your.xfm --s yoursubjectname --reg register.dat , but I get the following error message: tkregister2 --mov TDU__Blind_bef_JensenBruun_stat_TDU-Sens_TDU.mnc --xfm pet2tal.xfm --s jensen_ole_b --reg register.dat INFO: reading xfm file pet2tal.xfm, trying as MINC xfm regio_read_mincxfm: No such file or directory Could read pet2tal.xfm Does anyone know what to do? Thanks, Carsten

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Does 'color scale bar' show the cortical thickness or [-log10(p)]?
by Ruiwang Huang 10 May '07

10 May '07

Dear All, I am puzzled by the meaning of 'color scale bar', which appears in the first figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure? Many thanks in advance Rhuang

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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/

2 1

(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

2 1

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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Freesurfer May 2007