Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Baby's cortical ribbon?
by Eggebrecht, Adam 30 Mar '11

30 Mar '11

Hello there, Is FreeSurfer able to extract the neonatal cortical ribbon? Typically babies have a much better contrast with their T2 than with their T1. I know FS uses the T1 so I assume babies are not well handled by the usual processing. If not FS, are you aware of another suite which can extract the cortical surface for babies, or using the T2? Many thanks! Adam Adam T. Eggebrecht, Ph.D. Dept. of Radiology Washington University School of Medicine St. Louis, MO 314-362-6942 The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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2 x 2 x 2 design
by Jose Luis Cantero Lorente 30 Mar '11

30 Mar '11

Dear Doug, I would like to be sure that I've understood the rules for the following contrast in a 2x2x2 design with diagnosis (D1, D2), gender (Male, Female) and handedness (Left, Right) as discrete factors. D1MaleLeft D1MaleRight D1FemaleLeft D1FemaleRight D2MaleLeft D2MaleRight D2FemaleLeft D2FemaleRight interaction between Diagnosis, Gender, and handedness [ 1 -1 -1 1 -1 1 1 -1] interaction between Gender and handedness for D1 [ 1 -1 -1 1 0 0 0 0]/2 interaction between Gender and handedness for D2 [ 0 0 0 0 -1 1 1 -1]/2 interaction between Diagnosis and handedness for Males [ 1 -1 0 0 -1 1 0 0]/2 interaction between Diagnosis and handedness for Females [ 0 0 1 -1 0 0 -1 1]/2 interaction between Diagnosis and Gender for Left [ 1 0 -1 0 -1 0 1 0]/2 interaction between Diagnosis and Gender for Right [ 0 1 0 -1 0 -1 0 1]/2 Thanks in advance, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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Re: [Freesurfer] Recon-all and CT/SPECT images‏
by Marie ERESUE 30 Mar '11

30 Mar '11

Hi Bruce, thank you for your answer. I did recon-all with my CT and SPECT recon-all -i home/pmod/Bureau/freesurfer/subjects/... -subjid ... and then, I tried to register CT with MNI with bbregister: bbregister --mov MNI152_T1_2mm_brainnii --s image1_CT/ --init-fsl --reg ct_recal_mni.dat --bold But I have an error: mri/brainmask not found into CT folder, like if recon-all didn't work. best regards, Marie

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Bad orientation/registration in the motion correction step
by Nikolas Borrel-Jensen 30 Mar '11

30 Mar '11

Hi! I am having some trouble with the motion correction step when having two volumes (NIFTI files). The average volume has not been determined correctly due to a wrong orientation/registration of the two original volumes (see http://freesurfer.nikolasborrel.com/bad_registration.tif) Is the problem caused by wrong information in the qform matrix in the header of the NIFTI file or by a bad registration in the mri_robust_template or mri_convert functions in the motion correction step? Kind regards Nikolas Borrel-Jensen

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Recon-all and CT/SPECT images
by Marie ERESUE 30 Mar '11

30 Mar '11

Hi, I try to use the command "recon-all" with my CT and SPECT images, like my IRM, but I have this error message: talaraich failure detection: ERROR talarach_afd: talarach transform ... thanks marie

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(no subject)
by Gabriel Go.Es. 30 Mar '11

30 Mar '11

Dear FS experts, I would like to be sure that I've understood the rules for the following contrast in a 2x2x2 design with diagnosis (D1, D2), gender (Male, Female) and handedness (Left, Right) as discrete factors. D1MaleLeft D1MaleRight D1FemaleLeft D1FemaleRight D2MaleLeft D2MaleRight D2FemaleLeft D2FemaleRight interaction between Diagnosis, Gender, and handedness [ 1 -1 -1 1 -1 1 1 -1] interaction between Gender and handedness for D1 [ 1 -1 -1 1 0 0 0 0]/2 interaction between Gender and handedness for D2 [ 0 0 0 0 -1 1 1 -1]/2 interaction between Diagnosis and handedness for Males [ 1 -1 0 0 -1 1 0 0]/2 interaction between Diagnosis and handedness for Females [ 0 0 1 -1 0 0 -1 1]/2 interaction between Diagnosis and Gender for Left [ 1 0 -1 0 -1 0 1 0]/2 interaction between Diagnosis and Gender for Right [ 0 1 0 -1 0 -1 0 1]/2 Many thanks in advance, Gabriel

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problem of correction for multiple comparisons in surface based analyses
by Habets P (SP) 29 Mar '11

29 Mar '11

Hi, This is probably a question for Doug Greve, Which is to most preferably correction for multiple comparisons when investigating surface based cortical thickness changes between groups in smoothed data. Furthermore subjects between groups are related in other words not independent from each other. It is not clear for me whether FDR or cluster wise correction is feasible in highly smoothed and data that does not fulfill the criteria of independence. Best wishes, Petra Habets [cid:image001.jpg@01CBEE1C.2A94F050] Petra Habets PhD-Student School for Mental Health and Neuroscience p.habets(a)maastrichtuniversity.nl <mailto:p.habets@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl> Vijverdalseweg 1, 6226 NB Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T + 31 43 368 8659 F + 31 43 368 8689 Note: the email addresses have changed! [cid:image002.jpg@01CBEE1C.2A94F050]Please consider your environmental responsibility before printing this e-mail.

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ROI-based fixed effect analysis
by Qi Zhu 29 Mar '11

29 Mar '11

Hi, Sorry for posting again. I just want to get the average ces and cesvar values across subjects (fixed effect) for a specific ROI, and then run some statistics on them. Can I just average the gamma and gammavar that in the osgm folder after I ran the voxel-based ffx group analysis in my group data defined ROI to get those values? And how to average the gammavar values in a ROI? Just mean(gammavar), or sqrt(mean(gammavar^2))? Thanks very much for the answers. regards, Qi Zhu Laboratorium voor Neuro- en Psychofysiologie K.U.Leuven Medical School

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Re: [Freesurfer] reg-feat2anat problem
by Douglas N Greve 29 Mar '11

29 Mar '11

That would be the same as specifying highres.nii.gz as the intermediate registration (--int to bbregister). Is this what you tried? doug Cris Lanting wrote: > Dear all, > dear Doug, > > >> If you have a partial FOV, then it >> will probably fail. You can test this by running bbregister outside of the >> reg-feat2anat. You can look in the reg-feat2anat for a command line, but it >> should be something like: >> >> bbregister --s subject --mov example_func.nii.gz --bold --init-fsl --reg >> register.dat >> >> If this fails, you have a couple of options. If the functional and >> anatomical were acquired in the same session, then you can use --init-header >> instead of --init-fsl. If they are not but you have a full-brain of anything >> acquired during the same session as the functional, you can pass that as an >> intermediate volume to bbregister (--int). >> >> doug >> >> >> > > I've tried the --init-fsl option and the --init-header but they both > seem to fail. I noticed that there is a --init-reg option; > Is it not an idea to normalise the T1 (mprage) file called > highress.nii.gz (output registerT1.dat) and then in a second step > apply this to a previously registered file > (example_func2highres.nii.gz) using the --init-reg option? > > so, in short, would this approach work? > example_func.nii.gz -> example_func2highres.nii.gz (using flirt or > anything that works) > bbregister --s subject --mov highres.nii.gz --T1 --init-fsl --reg registerT1.dat > bbregister --s subject --mov example_func2highres.nii.gz --bold > --init-reg registerT1.dat --reg registerfunc.dat > (ps, I haven't tried this yet...) > > Or are there other options.... > > Kind regards, > Cris > > > -- 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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reg-feat2anat problem
by Cris Lanting 29 Mar '11

29 Mar '11

Dear all, I'm having a slight problem with reg-feat2anat to transform functional data (FSL) to anatomical (Freesurfer) in that the resulting transformation seems completely wrong. What I've done so far is the following: 1) run FEAT including the normal FEAT registration (which I know fails due to a lack of FOV in the functional data) 2) re-run the Flirt for a proper registration (i.e. by using the -usesqform option to obtain better registration) 3) overwrite the example_func2highres.mat, highres2standard.mat and example_func2standard.mat file with the newly obtained registration files. (The resulting files are now properly registered when viewing in e.g. fslview) 4) Run updatefeatreg <featdir.feat> 5) Start FEAT and change the mode to run Post-stats only. Select the FEAT output directory as input. Go into the registration tab and turn off all registration. Press GO. (steps 3-5 following the FSL FAQ on custom registration into a FEAT analysis) 6) run a complete freesurfer segmentation and all the rest using recon-all etc 7) reg-feat2anat --feat featdir.feat --subject subjectid When I now check the registration, it seems completely wrong... My guess would be that it has to do with the re-registration in steps 2-5 but as far as I can tell the files are registered properly to the anatomy scan (and to the template (or standard), the MNI152_T1_1mm_brain file) Any ideas? (Not sure whether it is appreciated if I send a screenshot as attachment, so I'll leave it for now) Cheers, Cris

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