Freesurfer

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30132 discussions

questions about: fix bad talairachs tranforms
by liyari5018 22 Apr '10

22 Apr '10

Hi freesurfer experts: 1\ when I finished the first step of recon-all(-autorecon1), check with tkregister2, do i need to check each slice or I just need to check few key anatomicals (Anterior / posterior commissures, the temporal lobes in the coronal plane, and the midline cut)? I think a lot of work to do so, and difficult to control. Is that necessary to do this for every subject? 2\ when I finished fixing bad output from the talairachs registration, click the SAVE REG button, and I should rerun : recon-all -autoreon1 -subjectid subjectname or next command ?

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skull stripping error?
by Wenger, Elisabeth 22 Apr '10

22 Apr '10

Dear freesurfer specialists, we just ran a sample of 91 subjects (with 3 timepoints), and in 5 of them the following problem occured: freesurfer exited with error in autorecon1 during skull stripping. The protocol looks like this: #-------------------------------------------- #@# Skull Stripping Thu Sep 17 18:13:23 CEST 2009 /Applications/freesurfer/subjects/1115is05B/mri \n mri_em_register -skull nu.mgz /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta \n aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (51, 10, 25) --> (205, 255, 237) using (102, 92, 131) as brain centroid... mean wm in atlas = 126, using box (83,62,105) --> (120, 122,157) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Darwin LIP-bxp-164-3.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 recon-all exited with ERRORS at Thu Sep 17 18:14:19 CEST 2009 We are pretty much freesurfer beginners and don't have a clue what kind of mistake this could be. We couldn't find any obvious differnces to our other subjects which ran fine. I also attach the whole recon-all.log file, just in case a problem occured on a previous stage we didn't recognize. We used a MacPro3,1 and Freesurfer version 4.2.0. Thank you for your help! Best, Elisabeth and Genia

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extract time series on surface
by GREGORY R KIRK 21 Apr '10

21 Apr '10

Hi, i want to extract epi time series on the surface, seems if i want every last drop of accuracy from bbregister i will need to run bbregister --mov epi_i_.nii --bold \ --s fbirn-anat-101.v4 \ --init-fsl --reg register_i_.dat on every epi volume in the time series and then mri_vol2surf --mov epi_i_.nii \ --reg register_i_.dat \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.epi_i_.mgh or else if i just use the linear reg (flirt or something ) to the first epi and use the bbreg transform to the first for all the others i might as well just be doing linear registration, i.e. losing the power of bbreg on all the others. then of course you have the problem of manually? checking all 300 or whatever registrations for the time series X number of subjects, or some auto method to check for time series outliers as a way to see what registrations may have gone of the track, but thats another story or am i missing something ? thanks greg

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other color map for a volume in freeview..
by Gonzalo Rojas Costa 21 Apr '10

21 Apr '10

Hi: Freeview only has grayscale, heat and jet in the color maps for a volume... How can I specify another color map ?... Sincerely, Gonzalo Rojas Costa

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Define ROI in individual surface based on area around a Talairach coordinate?
by Dickinson, Annelise (NIH/NIMH) [F] 21 Apr '10

21 Apr '10

Hi all, Is there perhaps a tksurfer tutorial for how to define and/or draw an ROI on an individual's surface by dilating out from a given Talairach coordinate? Freesurfer's volume registration is excellent and we'd like to use the correspondence to those normalized Talairach coordinates. Any insights or suggestions would be greatly appreciated! Thank you so much, hope you are having a good week! Best, Elise ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

1 0

Loading flattened surface in matlab
by f.leone＠donders.ru.nl 21 Apr '10

21 Apr '10

Hi everyone, I would like a 2D representation, hence a flattened version, of a surface in matlab, either the indices (a 2D map of 3D coordinates) or the actual values. Is this at all possible and if so, how? I see that read_surf gives vertex-indices back, but there is no 2D structure in there and MRIread is made for 3D-data only it seems. This post (which has similar aims as I have) http://groups.google.com/group/mvpa-toolbox/browse_thread/thread/dff9ba1008… suggests it isn't possible at all. And that it has serious disadvantages (the flattening process creating deformations of its own, which makes sense). That would be a pity. Then the best way would be to use the masked version of the 3D data: for that I can use the vertices given by read_surf, or is there an alternative/easier way? Hope it is possible, thanks a lot in advance, kind regards, Frank -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

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Spatial relation between brainmask and pial surface
by Milakara, Denny 21 Apr '10

21 Apr '10

Hi Bruce, Doug and community, When I compare brainmask (exported es nifti) with ascii pial surface it seems that brainmask(XZY) = ascii(XYZ), where the point of origin in the brainmask must be set to 128,128,128. Is this correct? If so, what is the maximal aberration expected in millimeters per axis and how to calculate it? Cheers, Denny

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Re: [Freesurfer] negative thickness value problem
by EK Kim 21 Apr '10

21 Apr '10

Hello Nick. I'm really sorry for bothering you but I'm still waiting for your answer. :) Thank you 2010/4/6 eunkyung kim <ksea03(a)gmail.com>: > Hello Nick. > Bruce said you can give me the latest Freesurfer version. > Actually, as I already mentioned, I have a problem with negative > cortical thickness and it bothered me very much.. > but it's fixed in the most recent version of mris_make_surfaces and > mris_thickness. > Freesurfer wiki homepage doesn't contain fixed version.. > I know you are very busy, but May I receive a fixed version from you > as soon as possible? > > Thank you. > > Sincerely, EK > > > 2010/4/2 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >> Hi EK, >> >> Nick (ccd) can get you the new versions. >> >> cheers, >> Bruce >> >> On Fri, 2 Apr 2010, eunkyung kim wrote: >> >>> Hi Bruce. Thank you for your reply. >>> But I still wonder because I used the most recent version ' >>> freesurfer-Linux-centos4-stable-pub-v4.5.0'. >>> Did you mean future released version 5.0 ? >>> Please let me know right place that obtain the 'mris_make_surfaces' >>> and 'mris_thickness' files. >>> The released note page does not contain this files at now... >>> >>> >>> Sincerely, EK. >>> >>> >>> 2010/4/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>> >>>> Hi EK, >>>> >>>> this was a bug I fixed a little while ago. The negative thicknesses >>>> should >>>> all be in non-cortical regions, but it's fixed in the most recent version >>>> of >>>> mris_make_surfaces and mris_thickness. The negative value should all be 0 >>>> >>>> cheers, >>>> Bruce >>>> >>>> On Thu, 1 Apr 2010, eunkyung kim wrote: >>>> >>>>> Dear all >>>>> I performed recon-all -s subjectID -qcache and obtained thickness data >>>>> which was normalized to fsaverage template. >>>>> I'd like to extract thickness value of the '-rh(or >>>>> lh).thickness.fwhm0.fsaverage.mgh' file in each subjects, so it was >>>>> transformed to the ascii file format. >>>>> However, the thickness data obtained from the ascii file did have some >>>>> negative values. !!! >>>>> Interestingly, the thickness value that was not normalized to the >>>>> fsaverage did not have negative values so I was very confused.. >>>>> Please let me know how can I treat the negative value. >>>>> >>>>> I really THANK YOU for your reply. >>>>> >>>>> Sincerely, EK. >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >

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intensity normalization and control points
by Jones, Kathryn L 20 Apr '10

20 Apr '10

Hello FS listers, I apologize if this has been asked before and I missed it in the archives. Can you use control points to correct intensity in overly bright scans. I've attached an example pic. Thanks for your help, Kathy

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normal value of "Brain Segmentation Volume Without Ventricles" value ?
by Gonzalo Rojas Costa 20 Apr '10

20 Apr '10

Hi: I need to know which is the value of BrainSegVolNotVent (Brain Segmentation Volume Without Ventricles) of healthy volunteers at different ages... Any paper ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile

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