Freesurfer

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21 participants
30070 discussions

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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aseg visualization question
by Morgan Hough 16 Apr '07

16 Apr '07

I have a quick question about an error we are getting with FS 3.0.5 when we are using tkmedit as described in the tutorial to display the segmentations overlaid on the T1. tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz The first error seems to regard the new requirement that a color LUT be passed with the segmentation option. If we add tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz tkmeditColorsCMA Then the message reduces to a problem of opening the segmentation file which it says is not in the right .cor format. I assume this is a legacy error message but I am not sure if I need to rename the aseg.mgz file or pass in another option with the file type. Thanks in advance for your time. Cheers, -Morgan

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Scripting: Feeding arguments and variables to script?
by Graham Wideman 16 Apr '07

16 Apr '07

Folks: Basic scripting questions: 1. When you launch FS from command line and provide a -tcl command to invoke a tcl script, how do you supply arguments to that script (or is that even possible)? FWIW, I tried things along the lines of: set myvar [lindex $argv 1] ... and this gives an error about "no such variable". 2. Once a script is running, what variables can it look at to find out: Current subject id Path to current subject Details about currently loaded surfaces: especially right or left 3. What assumptions, if any, can a script rely on as to current directory? Thanks, Graham

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Color threshold in freesurfer
by Doug Greve 16 Apr '07

16 Apr '07

Kevin has just made a change to the default way that the DEV version of tksurfer displays colors in overlays. The change has to do with the way the color is displayed near the threshold (fthresh). Previously, as a superthreshold value approached the threshold, its color and opacity would change. The result was that voxels at or just above threshold would be transparent, making them look like they were not active. The default now is to make them opaque regardless of value (as long as they are above threshold). When you look at the overlay configuation GUI, you will now see three items under "Threshold": Linear Linear Opaque Piecewise By default, "Linear Opaque" will be checked. To use the old behavior, check "Linear". Note that you can still control the overall opacity with the slider at the top of the GUI. Kevin is working on changing tkmedit. I'll let you know when that is ready. doug -- 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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