Freesurfer

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30076 discussions

differences between parcellation and node-by-node
by Goldman, Aaron (NIH/NIMH) [C] 20 Apr '07

20 Apr '07

Hi, I've been looking at thickness data and Freesurfer, and had a question about the process. I initially compared thickness in our two groups on a node-by-node basis using: mris_preproc --fsgd_file file_name --target average --hemi rh --meas thickness --out rh.thickness.mgh mri_surf2surf --hemi rh --s average --sval rh.thickness.mgh --fwhm 10 --tval rh.thick_smooth.mgh mri_glmfit --y rh.thick_smooth.mgh --fsgd file_name doss --glmdir average/glm/rh --surf average rh --C contrast.m with the fsgd file containing inputs like: Input name1 NC-male 31.34 etc. (the number at the end being age) I also tried running GLM on the average label thicknesses in the parcellation stat files to see how similar the results would be. I did this by reading the values in the ThickAvg column into SPSS, and using group and gender as fixed factors with age as a covariate. Doing it this way, several labels came up significant that contained few or no significant nodes doing it the other way. Since this was surprising, I was wondering if there was anything that might be expected to cause this difference. For example, could there somehow be a scaling factor applied to one analysis but not the other? Thanks, -Aaron-

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Coordinate Systems
by Mishkin Derakhshan 20 Apr '07

20 Apr '07

Hi, I am new to FreeSurfer and even after having read the wiki, I have a few questions regarding the coordinate systems. 1. What coordinate system do the final surfaces have. ie. mris_convert rh.pial rh.pial.ascii will list the coordinates in what space? 2. Are the coordinates of T1.mgz and rh.pial for example the same, or does tkmedit compute transforms on the fly so that everything is aligned properly when you view it. 3. What transform (or combination of transforms) will get me from the final surfaces coordinates, to the MNI talairach like space (which I think is called avg305). many thanks, mishkin

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pial surface question
by Turner, Jessica 20 Apr '07

20 Apr '07

Hi there-looking through the archives for pial surface questions I didn't see an answer to this: I've done autorecon1 and autorecon2 on this subject and I was checking the brain mask, wm, etc. There's a tip of temporal lobe lying outside the pial surface (red line), see attached, where the red cross is in both pictures. What are we supposed to do in this case? I can't put control points outside the red line, as I understand it? Thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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inflated surface QA check
by Turner, Jessica 19 Apr '07

19 Apr '07

Ok, should I be concerned about the little pimples on the rh inflated surface (see attached)? The left hemisphere on the same subject tends to be much smoother. If it's worthy worrying about I'll put the effort in to identify it on the wm.mgz and figure out what to do about it, but if not I'll ignore it. What would you do? Many thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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one image in the freesurfer tutorial 2006-05-30 pn.pdf
by Chuan.Chih.Yang＠rwth-aachen.de 19 Apr '07

19 Apr '07

Dear freesurfers, Here is the question about one page of the freesurfer tutorial (FreeSurferTtorial-2006-05-30pn.pdf). Page 87/202 , the top image, image after mri_ca_normalize (subcortical inentsity normalization), is this image with skull ? (coz it seems like the same as the one on page 86, after cortical skull stripping) coz after skull stripping, should it be without skull? Thank you in advacne for answering! Best regards, chaun-chih

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RE: [Freesurfer] Grainy thickness ribbon
by Jenni Pacheco 19 Apr '07

19 Apr '07

Hi Burak, Your best bet is to keep this question going to the list. I'll leave it for Bruce, or Doug, or Nick to answer. Jenni _____ From: Burak Ozkalayci [mailto:burak.ozkalayci@ugent.be] Sent: Thursday, April 19, 2007 7:11 AM To: Jenni Pacheco Subject: Re: [Freesurfer] Grainy thickness ribbon Hi Jenni, In fact no. I need a ribbon whose voxel values are assigned according to the cortical thickness. the mri/?h.ribbon.mgz is just a binary mask for the ribbon (as you can check from the cortical thickness ribbon images I attached to my former mail). I think that the -fillribbon option for the mri_surf2vol function does not work properly when the pial surface is selected like: mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon --surf pial the ribbon is filled in the normal directions of the surface which seem to give correct results for the white surface but for pial surface the direction of the normals should be reversed I think. By comparing the images I attached to the former mail, you can see that the filled ribbon from the pial and the white surface is different. I hope I could make it clear. Thanks again for any response, help. Burak Jenni Pacheco wrote: Hi Burak, I'm not really sure what you are trying to do, but a cortical ribbon is generated as part of the recon process, mri/?h.ribbon.mgz. Perhaps this is what you are looking for? Jenni -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of burak ozkalayci Sent: Wednesday, April 18, 2007 6:39 AM To: Freesurfer Mailing List Subject: [Freesurfer] Grainy thickness ribbon Dear surfers, I try to get a thickness map of the cortex by using the mri_surf2vol function. However when I used it like : mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon it generates a very grainy map. I think that those unassigned voxels are not hit by the normals of vertices on the white surface. To compensate it I tried to fill the ribon with the normals originated from the pial surface by : mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon --surf pial however the ribbon I get is shifted to the outer side of the cortex. I think the normals of the pial are oriented to show outer space of the cortex and they hit the voxels at the outerspace. I also attached the thickness maps of the ribbon I get from the white and the pial surfaces and the T1 image. They are the same slice of the volume, and you can see that pial one passes beyond the pial surface in general. In the help of mri_surf2vol for the fillribbon option, it is explained as "iterate projfrac from 0 to 1". And when the code is running I saw that iteration has a 0.05 step. I wonder whether is it possible to define the stepsize and the range for example 0 to -1 to reverse the hitting voxels. Thanks in advance. Burak

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tksurfer - list overlay values inside a label
by raij＠nmr.mgh.harvard.edu 18 Apr '07

18 Apr '07

Hi Doug & Kevin, I am trying to save a text list from tksurfer that contains all the overlay values (one value per each vertex point) inside in a functionally defined label. The labels were originally defined from a different data set than the overlays where I need the values. The overlay where I want the values picked from is in the format of a series of spherical surface files (ico7): *_time005-tau-lh_000.bfloat *_time005-tau-lh_001.bfloat *_time005-tau-lh_002.bfloat *_time005-tau-lh_003.bfloat *_time005-tau-lh_004.bfloat *_time005-tau-lh_005.bfloat *_time005-tau-lh_006.bfloat Notice that our overlay does not have the usual h-lh.bhdr files that would collect all the time frames and contrast conditions (this is after some custom post-processing) so we have to access the *000.bfloat -> *006.bfloat files directly. Not sure that matters though. Any suggestions how to come about this? I tried to look at the tcl scripting reference but did not quite see what I needed there (or then I just did not understand what I read :). Thanks!!! -Tommi

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question re: white matter edits
by Turner, Jessica 18 Apr '07

18 Apr '07

Hi there experts-When we load up wm.mgz with the lh.white and rh.white on one subject, the white matter mask overlaps into the the gray matter ribbon (see attached). When we look at the T1 underneath it, the red and green lines look just fine, but the white matter mask is a bit generous. Do I need to clean that up? Thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

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3T sequence
by Kirk, Gregory 18 Apr '07

18 Apr '07

Hi, we just got our 3T Siemens scanner and I was lookinging for the recomendations on sequence and protocoll parameters that are sugested for data acquisitions to give best results with freesurfer segmntation/cortical recon etc. It seems there was a web page that had the suggested best for this but I can't seem to find it. Is there something still around ? thanks Greg.

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Total brain volume, correlation coefficient after GLM
by zheng.hui＠singhealth.com.sg 17 Apr '07

17 Apr '07

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