Freesurfer November 2014

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

Re: [Freesurfer] tksurfer curvature and overlay displays
by Graham Wideman 25 Nov '14

25 Nov '14

At 11/24/2014 08:23 AM, Bruce Fischl wrote: >Hi Graham > >have you tried freeview? We stopped development on the tktools some time >ago. > >cheers >Bruce Hi Bruce, thanks for replying. Yes, I did proceed to try the same task in Freeview (which in general has a nicer UI, to be sure). Some notes: Test case: For subject bert, display principal curvature k1 (of smoothwm) on smoothwm and on inflated. Using Freeview latest version, in Linux Mint 15. Freeview Problems/Bugs ----------------------- 1. The Threshold frequency histogram widget with color adjustment handles is a great idea, but has several problems. a. Horizontal range of the freq hist defaults to entire range of the variable, which, for k1, is one to two orders of magnitude larger than the range of the bulk of the data. Consequence: the bulk of the data appears compressed to a tiny range near zero, in a tiny number of bins, and it's impossible to set the adjustment handles. This mechanism needs to accept manual upper and lower limits (and options to clip outliers to that value, or exclude them). b. The "Use percentile" checkbox doesn't seem to do anything that I could discover. c. The mouse hit detection for selecting and dragging the color adjustment handles often doesn't work. This is some combination of: -- The target area of the handles is too small. -- Clicking the handle but missing instead moves some other handle to the clicked location -- Sometimes the hit detection seems to think you're pressing/clicking on the mirror-image side of the graph. Press at +10, and it's like you pressed at -10. 2. It would be great to be able to clone (or save/load) display settings associated with one surface onto another. This way, time spent configuring the display of a particular variable on, say, smoothwm, would not have to be redone (inevitably imperfectly) to display the same variable on another surface like inflated, which is a frequent need. mris_convert ------------- 3. crv->text, text->crv. I didn't find a tool that would convert between crv and text format and back, to make it easy to use some other tool to clip k1 to tractable limits. Maybe mris_convert does this, but if so, the help for that program could use some revision: --------------- Usage: mris_convert [options] <input file> <output file> ... -c <scalar file> input is scalar curv overlay file (must still specify surface) --------------- a. 'curv' perhaps also includes 'crv'? b. Why is 'surface' needed? The curv/crv files contain everything they need for conversion. Requiring surface makes it seem like the conversion is going to do something more elaborate than just convert binary <--> text. c. And does 'surface' mean just an argument like 'orig' or 'pial', or the name of a surface file? Perhaps it just means that mris_convert still looks for an <input file> argument, but doesn't use it? Anyhow, I didn't trust that this was going to do what I intended. ------- I DID end up getting the display I wanted: I inspected a k1.crv file in a hex editor, discovered it was the same as old "new" .curv format, and wrote some python code to read/write/filter such a file. With this I could produce a clipped version of k1, which did work tractably in Freeview and produced a nice display. -- Graham

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Digest mode for mailing list and responding to mails
by Janosch Linkersdörfer 25 Nov '14

25 Nov '14

Hi list, I recently switched to the digest mode for the mailing list. Since then, I don't receive answers to my mails as mails anymore, making it harder to respond to them (or any other mail on the list). Does anybody experience the same issues? How did you solve them? Thanks, Janosch

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Freeview in a VM (Debian)
by Elena Molina 25 Nov '14

25 Nov '14

Hi all, I am running FS in a VM (Debian, wheezy) and I would like to create a 3D reconstruction of the hippocampus in .png. For that, I executed the following code lines: >> mri_extract_label aseg.mgz 17 lh.nii >> mri_extract_label aseg.mgz 53 rh.nii >> freeview -slice 500 500 500 -v lh.nii:isosurface=on rh.nii:isosurface=on -viewport 3d -cam azimuth -90 elevation 25 dolly 5 -ras 0 0 10 -ss 3dhipo.png But I have an error with the freeview command: freeview.bin: cannot connect to X server How can I solve it? Is there another way to generate the .png? Best Regards, Elena

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Freesurfer Version
by Cristian Patrick Zeni 25 Nov '14

25 Nov '14

Gentleman Which Version of Freesurfer should I download for use with the OS X Yosemite 10.10.1? Thanks Cristian

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TRACULA- DKI?
by Cat Chong 25 Nov '14

25 Nov '14

Dear Tracula Team, Quick question: Is Tracula able to to process diffusion kurtosis data, and yield, let's say, 'mean kurtosis' parameters for specific fiber tracts?cheers,Cat

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Tracula mri_convert error
by Janosch Linkersdörfer 25 Nov '14

25 Nov '14

Hi experts, I wanted to play with Tracula. Strangely, already the first preprocessing step, i.e., conversion to .nii.gz, fails. Apparently, mri_convert (falsely) recognizes my dicom files as MGH dicoms ("This looks like an MGH DTI volume"). Could this be the reason why it fails? Thanks, Janosch

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Resample the surface mesh
by ting xu 24 Nov '14

24 Nov '14

Dear freesurfer experts, Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer? Many thanks, Ting

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Download of latest Tracula version not possible
by Janosch Linkersdörfer 24 Nov '14

24 Nov '14

Hi all, I am trying to download the latest version of Tracula from this site http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. This seems not to be possible at the moment. Are there server problems? Thanks, Janosch

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can I apply freesurfer significant clusters as ROI in fMRI study?
by chenchunhuichina 24 Nov '14

24 Nov '14

Dear freesurfer experts, I searched on the wiki but can not figure out how to solve this problem: I found some significant clusters on graymatter thickness, how can I use it as a ROI in my functional MRI study? I have both structure and function data of the same subjects, so I can either do it in stardard space or native space one by one if possible. Any help is appriciated~ Best 2014-11-20 Chunhui Chen _________________ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875

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pial mask
by Octavian Lie 24 Nov '14

24 Nov '14

Dear all, After running the recon-all on a subject, I needed to create a 'pial' surface to include the hippocampi, which are not included well in the pial reconstruction. So I generated a mask and used it to mask brain.mgz. 1. All well, except that in both the mask and the masked brain volume (readybrain.mgz, see below), the fill extends with a variable layer of about 1 voxel) above the pial red contour in some areas (see the top, leading me to believe that the red contours we use when editing are not the actual pial surfaces, but some interpolations of the actual calculated pial surface. If this is true, then there may be some editing errors when using these contours. Another explanation could be the resolution of the mris_fill. Please let me know which is the case, and how to fix it so that the mask closely follows the red contour. 2. I need to generate a surface from readybrain.mgz, preferably that can be registered to the sphere.reg and on which cortical parcellation (DK atlass) can be applied. Is there a way? If not, I would still like to know how to generate the surface of this volume. Thank you, Octavian Here is the code I used: cd /usr/local/fs5.3/freesurfer/subjects/subjid mris_fill -c -r 0.1 surf/rh.pial mri/rh.pial.filled.mgz && \ mris_fill -c -r 0.1 surf/lh.pial mri/lh.pial.filled.mgz && \ mri_concat --combine --i mri/rh.pial.filled.mgz --i mri/lh.pial.filled.mgz --o mri/pial.filled.mgz && \ cd ./mri && \ mri_binarize --i aseg.mgz --match 5 --match 9 --match 10 --match 14 --match 17 --match 18 --match 19\ --match 25 --match 31 --match 44 --match 48 --match 49 --match 53 --match 54 --match 55 --match 57\ --match 63 --match 86 --match 96 --match 97 --match 105 --match 106 --match 114 --match 115\ --match 195 --match 199 --match 203 --match 204 --match 205 --match 216 --match 222 --match 225\ --match 507 --match 557 --match 1200 --match 1201 --match 1205 --match 1206 --match 2200 --match 2201\ --match 2205 --match 2206 --o hippoamy.mask.mgz && \ fscalc pial.filled.mgz add hippoamy.mask.mgz -o epimask.mgz && \ mri_convert brain.mgz brain.float.mgz -odt float && \ mri_mask brain.float.mgz epimask.mgz readybrain.mgz

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Freesurfer November 2014