Freesurfer April 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
78 discussions

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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mri_convert, primary slice direction and resampling
by Julia Hamstra 17 Apr '07

17 Apr '07

Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected from right to left), but when I create files from mri_convert the header reads axial. This is particularly problematic when converting to analyze format from dicoms or another file type because the dimensions of the sagittal slices are applied the transverse plane. Using in_orientation and out_orientation options, the images will display correctly, but the header still reads axial. Can mri_convert subsample an image by retaining every other voxel without interpolating between voxels? Thank you, ~julia

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label ID in tksurfer
by Szymon Mikulski 17 Apr '07

17 Apr '07

Hi, I've created a script for my MEG data which uses surfcluster and tksurfer to output functionally defined labels. It also makes an image of the labels overlaid on the cortical surface. I was wondering if there is any way to have it automatically identify the labels in the image, say by printing the label-id next to the actual label outline. Thanks, Szymon

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tkmedit question
by Sebastian Moeller 17 Apr '07

17 Apr '07

Aloha FreeSurfers, I have a small question regarding tkmedit and the line tool. Is it possible to specify start and end point for a line on the tcl prompt? My goal is to create a line in a volume that is not parallel to one of the main axes. ATM I resort to turning the volume in question into a plane parallel to the line, but my overlays are not rotated accordingly so that is not as comfortable as I want it to be, and since it is somewhat exploratory pre-rotating volume and overlay is a bit unwieldy ;). For completeness, I am using 3.0.5 centos4-x86_64 under suse linux 10.1, but I guess that does not really matter. ahoi & thanks for supplying these nice & powerful tools Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Freesurfer April 2007