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30076 discussions

mris_anatomical_stats
by Catherine Hartley 11 May '07

11 May '07

Hi, I'm trying to get the anatomical statistics for a new parcellation, ? h.aparc.splitcingulate.annot, I've created using mris_divide_parcellation. I've tried using mris_anatomical_stats with various argument structures (specifying output filenames, not specifiying output filenames) and can't seem to get it to write a ? h.aparc.splitcingulate.stats file. It generates and outputs summary statistics, but it does not write a .stats file to the stats directory: [catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats mm103184 lh inflated -a mm103184/label/lh.aparc.splitcingulate.annot reading volume /Applications/freesurfer/subjects/reruns/mm103184/mri/ wm.mgz... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.inflated... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.pial... reading input surface /Applications/freesurfer/subjects/reruns/ mm103184/surf/lh.white... done. computing second fundamental form... ... done. total white matter volume = 516178 mm^3 total surface area = 81462 mm^2 total gray matter volume = 230187 mm^3 average cortical thickness = 2.175 mm +- 0.836 mm average integrated rectified mean curvature = 0.025 average integrated rectified Gaussian curvature = 0.096 folding index = 9766.477 intrinsic curvature index = 937.896 [catemac:freesurfer/subjects/reruns] cate% Thanks for your help! -Cate

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Fwd: [Freesurfer] mris_divide_parcellation
by Catherine Hartley 11 May '07

11 May '07

> From: Catherine Hartley <cate(a)nyu.edu> > Date: May 10, 2007 7:10:19 PM EDT > To: Doug Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mris_divide_parcellation > > then i get: Exec format error. Binary file not executable. > > [catemac:/Applications] cate% cd freesurfer/bin > [catemac:/Applications/freesurfer/bin] cate% chmod a+x > mris_divide_parcellation > [catemac:/Applications/freesurfer/bin] cate% mris_divide_parcellation > tcsh: /Applications/freesurfer/bin/mris_divide_parcellation: Exec > format error. Binary file not executable. > [catemac:/Applications/freesurfer/bin] cate% > > > > On May 10, 2007, at 6:58 PM, Doug Greve wrote: > >> try >> >> chmod a+x mris_divide_parcellation >> >> Catherine Hartley wrote: >> >>> Thanks! However when i try to execute the command, i get a >>> message saying "Permission denied". Any ideas? >>> >>> Thanks, >>> Cate >>> >>> On May 10, 2007, at 5:30 PM, Doug Greve wrote: >>> >>>> >>>> here you go ... >>>> >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> mris_divide_parcellation >>>> >>>> Catherine Hartley wrote: >>>> >>>>> Hi, >>>>> >>>>> I'm hoping to get a hold of the function >>>>> mris_divide_parcellation which automatically subdivides the >>>>> cortical parcellations for a region into sub-regions. It's >>>>> not a part of the current Freesurfer release but would it be >>>>> possible to get a copy of the development version? >>>>> >>>>> Thanks, >>>>> Cate >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>>> >>>> In order to help us help you, please follow the steps in: >>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >>>> >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >

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mris_divide_parcellation
by Catherine Hartley 10 May '07

10 May '07

Hi, I'm hoping to get a hold of the function mris_divide_parcellation which automatically subdivides the cortical parcellations for a region into sub-regions. It's not a part of the current Freesurfer release but would it be possible to get a copy of the development version? Thanks, Cate

2 3

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

2 1

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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