Freesurfer September 2007

freesurfer@nmr.mgh.harvard.edu

69 participants
99 discussions

about inflate the surface
by Ning Liu 07 Sep '07

07 Sep '07

Hi all, When I inflate surface, I find the results I get are different from someone's. The one that I get inflates like a filled balloon, but someone's seemed inflated not enough (especially in the TE). The parameters for mris_inflate command are same. I enclosed these two kinds of inflated surface. Would you please tell me why? Does it caused by the smoothwm file? Thanks a lot. Ning -- When was the last time you had a conversation with the moon or made a wish on a falling star? The time is now.

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wrong values for volume
by Rafael Huber 07 Sep '07

07 Sep '07

Dear Freesurfer Users I did the whole group analysis process, but unfortunately the measure for volume didn't work correctly. I think the problem is, that i couldn't create the "source-files" (the ?h.volume files in the /subject/surf folders) like for the other measures. I did that with a command in matlab, which Bruce Fischl recommended me. When i try to look at the results with the tksurfer the whole hemisphere is yellow and the values for the sig.mgh overlay are all 10000000000. Has somebody an idea how to create the volume measure otherwise, or what went wrong? Thanks for every help in advance. Best regards, Rafael Huber -- Rafael Huber Student Division of Neuropsychology Institute of Psychology University of Zurich

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Directed contrast in FS group analysis
by Juergen Haenggi 07 Sep '07

07 Sep '07

Dear Freesurfer users In order to be absolutely sure about the direction of a contrast I have the following question: gamma = 1*beta1 + -1*beta2 + 0*beta3 + .... Does beta1 always correspond to the class that is entered most superior in the fsgd file and beta2 to the class that is entered as the second class in the fsgd file? Do the other betas correspond to the variables listed from left to right in the fsgd file? Thanks for your confirmation. Best regards Juergen Haenggi ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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version 4
by Don Hagler 06 Sep '07

06 Sep '07

I processed some brains using version 4 and it seems that it took substantially longer than typical for version 3. It took about 3 days for one subject with version 4, compared to 1.5 days for the same subject with version 3.0.5. Is this on par with what others have experienced? At least for this one subject, the inflated surface looks a bit strange for version 4 compared to version 3 (see attached). I haven't yet done a side-by-side comparison for multiple subjects, so I don't know how reproducible this will be. _________________________________________________________________ Gear up for Halo® 3 with free downloads and an exclusive offer. http://gethalo3gear.com?ocid=SeptemberWLHalo3_MSNHMTxt_1

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atlas space question
by Lindsay Casmaer 06 Sep '07

06 Sep '07

Hello, Are the calculated volumes for the subcortical segmentations in atlas space? I am trying to verify if the registration is done in atlas and then rolled back to subject/native space, or if the volumes are calculated in atlas space. Thanks, Lindsay

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strange values in sig.mgh file
by Rafael Huber 06 Sep '07

06 Sep '07

Hy there We did a group analysis and some results were ok (like area, thickness), but others were not. When we tried to load the sig.mgh file of the volume measures the whole hemisphere was completly yellow and the vertices were much too large. We did the whole process with the files we got from the matlab command Bruce Fischl recommended us days before. (*) Meancurv was also not correct for both hemispheres, even if i did the same for lh and rh. (in the folder rh.Turner_meancurv.glmdir is only a mri_glmfit.log file) Thanks for every help! Best regards Rafael Huber - University Zurich (*) [thickness, f] = read_curv('lh.thickness') ; [area, f] = read_curv('lh.area') ; volume = thickness .* area; save_mgh(volume, 'lh.volume.mgz', eye(4)); [thickness, f] = read_curv('rh.thickness') ; [area, f] = read_curv('rh.area') ; volume = thickness .* area; save_mgh(volume, 'rh.volume.mgz', eye(4))

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(no subject)
by Steven Scholte 05 Sep '07

05 Sep '07

Dear All, I have been trying to apply tkregister to our FEAT data as registration using automatic FLIRT does not work accurately when only a couple of functional slices are recorded. I use the option --fslregout to create a FSL compatible transformation matrix, registering the example_funct to the subjects' highres brain. I use the following: tkregister2 --feat pp0009.feat --subject pp0009 --fstarg --targ brain --fslregout fslregoutpp0009 After the manual alignment I check the registration by first applying the transformation on the example_func with FLIRT as follows: /usr/local/fsl/bin/flirt -in /ext_drv/Weibull/test/pp0009.feat/example_func.nii.gz -applyxfm -init /ext_drv/Weibull/test/fslregoutpp0009.mat -out /ext_drv/Weibull/test/pp0009.feat/example_func_TRANS.nii.gz -paddingsize 0.0 -interp trilinear -ref /ext_drv/Weibull/test/pp0009.feat/reg/highres.nii.gz Fslview will not load this resulting image though, giving me the message: Error:: FslReadTimeSeries: voxel outside valid range Does anyone know what i did wrong? Any suggestion would be helpful. Regards, Steven

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cortical flattening
by Valentin Piech 05 Sep '07

05 Sep '07

Hi all, I think that there is a bug in mris_flatten of freesurfer version 4.0.0. It took more than 1000 iterations for each occiput patch of a subject, and they are getting flattened incorrectly. I went back to version 3.0.5, and the exact same patches are flattened correctly withing 200 - 300 iterations. I can upload pictures of the patches if you would like. Best, Valentin -- Valentin Piech, Graduate Fellow Gilbert Lab for Neurobiology & Reeke Lab for Biological Modelling Rockefeller University

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cortical flattening
by Natalia Bilenko 05 Sep '07

05 Sep '07

Hi all, I am having some trouble with creating cortical patches for one subject. Though 3d patches look normal, they are not getting flattened correctly, and mris_flatten takes an unusually long time. I tried re-creating the patches (both making new 3d patches and re-running mris_flatten), but I keep getting the same problem. The patches are very oddly shaped, and the curvature pattern on the full patches looks very bizarre. The subject's data is in /space/annecy_014/kdevaney/structurals/subj20. The names of 3d patches are lh.full.patch1.3d, rh.full.patch1.3d, lh.occ.patch1.3d, and rh.occ.patch1.3d, and the names of the flat patches are lh.full.patch1.flat, rh.full.patch1.flat, lh.occ.patch1.flat, and rh.occ.patch1.flat. Any suggestions? Thanks! Natalia

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searching for a method of declaring spherical ROIs in the volume
by Avram Holmes 05 Sep '07

05 Sep '07

All, I'm attempting to create some spherical ROIs around peak activated voxels in the volume. Is there anything similar to the label dilate function for use in the volume? Thanks for any help you can offer, Avram -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Freesurfer September 2007