Freesurfer

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30089 discussions

calculate percent from two different mgh files
by Knut J Bjuland 17 Oct '12

17 Oct '12

How can I dived a gamma.mgh with another gamma.mgh to get new mgh structure? Is there any Freesurfer Matlab function that I should use. I am able to use Matlab to calculate the difference for vol. n=size(gamm.vol(2)) for i=1:n; test=gamma.mgh.vol(i)/gamma.mgh(i) end I am trying to follow this howto at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07433.html. Knut J

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topology fixer removes connected white matter
by Benjamin Kay 17 Oct '12

17 Oct '12

I'm puzzling over why freesurfer is not including a chunk of white matter in the final surface and how I can fix it. The culprit appears to be the topology fixer. If you look at the attached screenshots, you can see that the offending bit of left frontal lobe is well-connected to the rest of the brain in wm.mgz (and, for completeness, filled.mgz). The yellow surface, which corresponds to lh.smoothwm.nofix, includes the desired white matter. Thus, neither tessellation nor smoothing would seem to be the problem. The green (white matter) and red (pial) surfaces from lh.orig exclude the desired white matter. Thus, I'm assuming the topology fixer is cutting off what it perceives to be a defect... but I can't figure out why or how to fix it. Although I will try, I do not expect that filling in the few missing white matter voxels or adding control points in that region will have any effect. Any other ideas?

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Editing Pial Surface
by Jonathan Holt 17 Oct '12

17 Oct '12

I'm wondering about how to best approach two similar problems with pial surfaces. In one case I'd like to extend it and in the other I'd like to reduce it (for lack of a better term) These first two images are from a brain in which I'd like to extend the surface. http://i.imgur.com/ziDQd.png http://i.imgur.com/i0sX3.png In this case focus on the bottom left and right corners of the cortex. You can see, especially in the second image (with aseg.mgz loaded), the pial surface cuts off part of the cortex on both sides. Interestingly, the pial surface seems to adhere to the aparc.mgz file, which is loaded and pretty clear in the first image, where the left out parts of the cortex are just labelled as 'none'. http://i.imgur.com/aUKiG.png http://i.imgur.com/4BRwv.png In the second case I want to edit the pial surface so it follows that gyrus toward the midline in the left hemisphere. In this case I've tried control points, specifically along the gyrus, and autorecon2-cp. I also tried to edit the parcellation along the gyrus for several slides followed by autorecon2 & 3. This didn't help anything, so I'm a bit stuck. You can see this brain follows the same trend as the last in which the pial surface follows the aparc.mgz, and the aseg.mgz seems more or less correct. Thanks and any help would be awesome! jon

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Talairach Failure Detection
by Daniel Ferreira 17 Oct '12

17 Oct '12

Dear experts, Please, I'm getting the Talairach Failure Detection problem in one of my subjects (message enclosed below). I tried to follow the tutorial to fix a bad Talairach with: 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I attach a screenshot. Both the standard and my MRI are slided down to the bottom of the window. See also attached tkmedit file. 2) Anyway, I tried also -notal-check to see if something changed in spite Talairach failed, but it fails also (off course). 3) I used -use-mritotal but I still get the same. However, this time processing finishes without errors, but my MRI is still at the bottom of the window and output cut all what is between middle temporal regions and neck. Please, any idea? Thanks a lot Daniel #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 /home/daniel/FreeSurfer/subjects/N001511_d2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC 2011 x86_64 GNU/Linux recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Changes to Sub-cortical Structures after adding WM control points
by Mark Fletcher 17 Oct '12

17 Oct '12

Dear FreeSurfers, After adding WMCP to a number of my subjects (which corrected the problem), I retrieved to cortical and subcortical volumes from my subjects using the "aparcstats2table". I had used "aparcstats2table" before and after adding the control points. Accurately, the regions I wanted to change, did change in volume. However, the subcortical volumes post WMCP changed a lot as well? Some regions changed more than 20% after adding WMCP to other regions? Is this normal? Should I go with the original "subcortical" segmentation volumes, or the new ones? Is this part of the known bug in version 5.1.0 mentioned in the release notes about "running recon-all" a second time? Please advise? Sincerely , Mark Fletcher

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Supratentorial volume vs brain segmentation volume
by Kwan, Justin 17 Oct '12

17 Oct '12

Dear Freesurfer experts, What is the difference between the supratentorial volume and brain segmentation volume? Does the supratentorial volume include CSF and ventricle volume? Thank you very much for your help. Best, Justin Justin Kwan, MD Assistant Professor Department of Neurology University of Maryland School of Medicine 110 South Paca Street, 3rd Floor Baltimore, MD 21201

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Functional labels from freesurfer
by ffmpeg ffmpeg 17 Oct '12

17 Oct '12

Hello! I was told that Freesurfer should generate labels for functional areas of the brain (for example, visual zones - V1, V2, etc.) when doing reconstruction (recon-all -autorecon-all). But the the label/ directory in output contains only these files: aparc.annot.a2009s.ctab aparc.annot.ctab lh.aparc.a2009s.annot lh.aparc.annot lh.cortex.label rh.aparc.a2009s.annot rh.aparc.annot rh.cortex.label which contain only anatomical labels. What could be wrong? If freesurfer does not generate those labels, is there some way to obtain them? (Obviously, I could create such labels by hand, but the result would be probably messy and imprecise.) Best wishes, Platon Pronko

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Problem with cortical GM vol (complete)
by Gabriel Gonzalez Escamilla 17 Oct '12

17 Oct '12

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Problem with cortical GM vol
by Gabriel Gonzalez Escamilla 17 Oct '12

17 Oct '12

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Re: [Freesurfer] DODS and group age interaction
by MAHINDA YOGARAJAH 17 Oct '12

17 Oct '12

Dear Doug, Many thanks for reply. Given the age-group interaction, and the fact that even when age is demeaned it simply means a difference in thickness will be tested for at age=mean age (as opposed to age=0) can I at least interpret the findings when using DODS model with age as a nuisance factor by saying that the difference in thickness between groups represents the difference between groups at the mean age across both groups. Beyond that limited interpretation, is there any other way to analyse the data ? Is there a another model I could use ? My age-group interactions are in a different location to the group differences - does this make any interpretation of group differences more robust ? Thanks. Mahinda

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