Freesurfer

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30132 discussions

different vertexes and faces on pial and inflated surface of the same hemisphere
by Forrest Sheng Bao 05 Apr '11

05 Apr '11

hi all, I encountered a strange problem today. I used recon-all -all to get surfaces of a subject. I have no problem with his/her left hemisphere. But for the right hemisphere, the numbers of vertexes and faces of pial surface are different from those of the inflated surface. I checked the headers of curavture and convexity maps also. They all tell the same information as the pial surface's header. But not the same as the header of inflated surface. I also checked the file content. The file did not seem like corrupted. I have never had the problem with other data i have. Only on this hemisphere of the subject. Has anyone out there experienced the same problem before? Cheers, Forrest

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edit volume remotely
by Sara Lozano-Zahonero 05 Apr '11

05 Apr '11

Dear all, We are trying to edit a new wm volume remotely. We want to substitute the mouse click with an external command. Since we are not familiar with tcl/tk we don't know where this action (mouse click to edit volume) happens within the script tkmedit.tcl. Could you please help us: How could we edit (or delete) voxel programmatically? The resulted wm volume should be saved for regenerating the surfaces with ?recon-all?. Thanks in advance for your help Sara

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N3 for improving cerebellum segmentation
by Tetiana Dadakova 05 Apr '11

05 Apr '11

Dear list, I have a question regarding intensity non-uniformity correction using N3 (as in Boyes et al, 2008). Does anyone have experience of using it for improving cerebellum segmentation, specifically distinguishing between white and grey matter in cerebellum? If yes, what are the best values for the options: -distance and -iterations? Cerebellum is very important for our study, therefore I am looking for ways of how to make the segmentation as good as possible. Thank you for your time and help, Tanja.

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help with CT scaling
by Andrew R. Dykstra 04 Apr '11

04 Apr '11

Hi all, I'm having problems either or converting a series of dicoms from a CT scan obtained at MGH main. When viewing them in the standard hospital viewer, they appear normal, but when viewing them in TKMEDIT (either the original dicom series or converted mgz file), the scaling changes. Are there any options in mri_convert I can use to overcome this problem? See attached view of the mgz file. Cheers, Andy

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resampling vol to surface
by GREGORY R KIRK 04 Apr '11

04 Apr '11

Hi guys, i am using the freesurfer-fsl integration to use labels from the freesurfer cortical surface as seeds for probtrackx probabilistic diffusion tractography. when the output of probtrackx is generated it is already in the freesurfer conformed space. I want to resample the output of probtrackx onto the cortical surface. I have the transformations from the diffusion data to freesurfer conformed space generated using bbregister to do the tractography but to use mri_vol2surf i need to first tranfrorm the output of probtrackx back into the epi space with the inverse of the bbregister tranform ( output in the fsl format) and resample it to the lower resolution epi resolution. i.e. there is not an option for mri_vol2surf to assume the data to be resampled onto the cortical surface is already in freesurfer conformed space. i suppose i could compute transformations from freesurfer conformed space to say brain.mgz, which would essentially be the identity transformation. mriconvert -it mgz -ot nii brain.mgz brain.nii i.e. bbregister --mov brain.nii --t1 -s subject -init-fsl --reg register.dat or i could make a fake identity transform like 1.0 1.0 ? don't know what this number is 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 round ? what should i use here. whats the best way to go here thanks greg

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Re: [Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain
by Douglas N Greve 04 Apr '11

04 Apr '11

Hi Scott, no there is not another space I would recommend. The cortical surfaces across subjects don't line up at all with a 12DOF transform. If you look at your activation in the volume along with surface lines, you may see that your surfaces intersect some of the activation but not others. I guess if the surface is showing your important activation, then it's probably ok. I've seen people do this before. doug Scott Burns wrote: > Doug -- > > >> After you've gone into MNI space with all of your subjects, then >> visualizing the results on the surface are of questionable value. >> > > All of our first-level and second-level statistical maps in MNI space and we wish to overlay them onto fsaverage, is there another space I could map these spmT images into that when overlayed would be more reliable/publication worthy? If this wouldn't work, what would you suggest? > > Scott > > > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Converting an FSL label to Freesurfer space
by mmoayedi 04 Apr '11

04 Apr '11

Hi, I'm trying to convert the individual FS parcelations to individual space in FSL. I'm not sure how to proceed. I've made a label from the individual subject's parcelation, and have saved it. How would I then convert the label to use it as a mask in the subject's structural space in FSL? Would mri_label2vol suffice? What would be my --reg? Thanks, Massih

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Questions about GLM, Random and Fixed Effects Analysis in FsFast
by Gabriel A. Tobon 04 Apr '11

04 Apr '11

Hello Freesurfers I would like to run a specialized group GLM analysis on the volume using estimates from the individual subject analysis in Freesurfer as summary statistics. I would like to learn a little more about how this estimation is done before doing so. I have looked at the documentation for "mri_glmfit" and the following tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial I also have your 1999/2003 manuscripts on "Signal Processing and Statistical Analysis for Event-Related fMRI" and "fMRI Analysis 101 - Univariate Analysis," but I am not sure if the method has been updated since then. * I noticed there is a weight matrix (W) described for "mri_glmfit" command. How is this derived and used? I can't find more information about it in the documentation/mailing list. * How are the nuisance regressors organized in the B matrix? I assume the conditions are first? What are the following regressors? * Do you have a similar manuscript that describes just how group analysis is implemented in FsFast? Thank you for your time and help! Gabriel

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mri_ca_register error
by T. Hagen 04 Apr '11

04 Apr '11

Hello all, I got this error message while running one of my subjects (freesurfer version 5.0.0): gcamFindOptimalTimeStep: Complete in 23335.062 ms 0388: dt=0.000000, rms=0.657 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Mon Apr 4 07:57:30 EDT 2011 /home/virtualuser/apps/freesurfer/subjects/flo/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s flo exited with ERRORS at Mon Apr 4 07:57:30 EDT 2011 The recon-all.log indicates that mri_ca_register couldn’t write the talairach.m3z file. The brainmask.mgz file is skull-stripped and the cerebellum is attached. There is enough disc space. Does anyone know what this could possibly mean and how to avoid it? Thanks in advance for your advice. Thomas Hagen

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Pial surface correction failure after adding control points
by Min Liu 04 Apr '11

04 Apr '11

Dear Freesurfer users, My first run of recon1&2 left some white and grey matter at temporal pole region excluded. So I edited the wm.mgz by adding a bunch of control points intending to get more white matter and expand the pial surface (please see the coronal slice in the attachment where the control points were placed). Then I ran the command 'recon-all -autorecon2-cp -subjid XX' WITHOUT '-autorecon3'. From my understanding, Freesurfer would recalculate the wm.mgz as well as the white matter and pial surfaces in temporal pole according to the control points. However, I got wm.mgz corrected and pial surface wrong (as the attached graph indicated). Did I do something wrong? Why wm.mgz got fixed while pial surface not? Thanks for help in advanced! Veronica

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