Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

quick follow-up
by Jared Price 04 Dec '08

04 Dec '08

Will missing header info affect the rebuild_gca_atlas script? I noticed it didn't like it if echo time, repetition time etc. didn't match. Also, I assume there is no difference, or minimal enough difference to ignore, in the 001.mgz file when converted from say nifti or straight from dicom. Correct?

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missing information in volume headers
by Jared Price 04 Dec '08

04 Dec '08

Dear freesurfer gurus, I noticed something unusual in some of our data today. When the command mri_info was run on some of the orig.mgz volumes the values listed for echo time and flip angle in some of the scans were 0.00, even though there was a listing for repetition time. What could have caused this? Could misinformation in the header cause variation in the freesurfer processing of that scan? Cheers, Jared

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vertex wise correction for multiple comparisons using permutation
by Lúcia Garrido 04 Dec '08

04 Dec '08

Dear Freesurfers, I'd like to correct for multiple comparisons vertex-wise instead of cluster-wise. Is it possible to do this using permutation (and not FDR)? I've seen in an e-mail from last year that the values of maximum statistic stored in the CSD file could be used for this purpose, and I'd be very grateful if you could let me know how. Many thanks, Lucia

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Creating a file with discrete locations with Freesurfer
by Andres Felipe Salazar Gomez 04 Dec '08

04 Dec '08

Good evening freesurfer list, I need to create a text file containing discrete locations in MRI coordinates (a group of points in the MRI images inside the brain, not on the cortex). I need this text file to be used in the mne_volume_source_space utility. The idea is using a discrete source space (based on the coordinates obtained from the needed text file) instead of the surfaces that are usually employed. I know I can get this text with Freesurfer but this is a new feature for me. Can anyone give me a clue on how to do this? Thank you for your help! -- Andres F. Salazar

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recon-all rerun
by Barkay, Gavriel 04 Dec '08

04 Dec '08

Hi, I ran recon-all -all crashed for reasons unrelated to FreeSurfer. I re-ran the analysis without -clean. Is the new skull stripped volume stored in brainmask.auto.mgz instead of brainmask.mgz? Thanks, Gabi

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Autorecon 1 y autorecon 2
by Kelly Silva 04 Dec '08

04 Dec '08

Hello, I´m having troubles with the first autorecon 1 and autorecon2. The script is attached. Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Re: [Freesurfer] CSF calculation
by Anthony 03 Dec '08

03 Dec '08

Hi Bruce, Thank you for your prompt reply ,guess I can only deal with GM an WM with freesurfer for now. I read somewhere in our archive that you were considering other approaches to compute sulcal CSF like using T2-images , will it be available for distribution ? Thanks, Anthony --- On Wed, 3/12/08, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] CSF calculation To: "Anthony" <slam_ono(a)yahoo.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Date: Wednesday, 3 December, 2008, 9:18 AM Hi Anthony, we compute ventricular CSF but not sulcal CSF (which you can't really see in a T1-weighted image). cheers, Bruce On Tue, 2 Dec 2008, Anthony wrote: > Dear all, > > Is there anyway to calculate CSF volume using freesurfer? I only know freesurfer supports GM and WM calculation based on aseg.mgz and aseg.stats . > > Thanks, > Anthony > > > > New Email addresses available on Yahoo! > Get the Email name you've always wanted on the new @ymail and @rocketmail. > Hurry before someone else does! > http://mail.promotions.yahoo.com/newdomains/aa/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer New Email addresses available on Yahoo! Get the Email name you've always wanted on the new @ymail and @rocketmail. Hurry before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/

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CSF calculation
by Anthony 02 Dec '08

02 Dec '08

Dear all, Is there anyway to calculate CSF volume using freesurfer? I only know freesurfer supports GM and WM calculation based on aseg.mgz and aseg.stats . Thanks, Anthony New Email addresses available on Yahoo! Get the Email name you've always wanted on the new @ymail and @rocketmail. Hurry before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/

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comparing hemispheres
by CARL＠nmr.mgh.harvard.edu 02 Dec '08

02 Dec '08

Hi Frederic, To amplify, are you are talking about vertex by vertex analyses in the context of between group comparisons? As Doug says, the optimal tools are not there yet. As you know, you can always drop the threshold on the other side and see if activations/thickness blobs emerge in the same areas on the contralateral side though this is not a formal statistical test of laterality. Of course there are the other simpler approaches if you are not talking vertex by vertex. If you have a result based on an mean thickness or fMRI activation in an aprior cortical parcellation (say, parsorbitalis) or an amalgam of such parcellations, then you are free to compare this with mean value from the same area in contralateral hemisphere, and formally test for a laterality interaction using a repeated measures GLM. But depending on what you want to do, even with vertex by vertex data there are some ways to interrogate your data more formally for laterality effects. Suppose you have a label/subregion/blub in one hemisphere (could be functional or structural) and you want to test formally for laterality ( formal two way interaction with side). You could draw by hand the mirror image of the blob in the other hemisphere either by anatomical landmarks or perhaps better, by recording the min and max tal coordinates in x,y,z (and some additional control points) for the hemisphere where you have your activation, flipping the sign of the x coordinate, and then marking the vertex in the other hemisphere that corresponds to the flipped tal coordinate. Then make a label of the mirror image blob, extract mean signal for each subject within boundries of said blob, AND run a glm on this with dx, gender or whatever else you are interested in. Notice if you do this, you are not biased in the same way you would be if you ran your test statistics based on individual subjects values extracted form the original hemisphere blob which would be circular. And I dont think, but you can check with Doug, that you are biased if you included a term for side and compare the original label with the mirror label as a repeated within subject factor, as long as you are not using the outcome of the analysis to test for the significance of the between group difference in the original hemisphere (which you KNOW HAS to be significant because thats how you defined the original label). But that bias would seem to be absent for the contralateral label. Carl -- Carl E. Schwartz, M.D. Harvard Medical School Director, Developmental Neuroimaging & Psychopathology Laboratory Psychiatric Neuroscience Program Massachusetts General Hospital tel 617-726-8965 fax 617-726-4078 On 12/2/08 11:19 AM, "Doug Greve" <greve(a)nmr.mgh.harvard.edu> wrote: We don't have a good way to do this yet. I've have been working on one but have dropped the ball. Some people will analyzed both the correctly-oriented data and left-right reversed for each subject, but this is not the best way to do it. doug Fr?ede?ric Andersson wrote: > Hi, > > Is there any way to compare left vs right hemisphere (surface morpho. > and functional data). I mean, is there any function to flip one > hemisphere in order to compare it with the other one? > > Thanks, > > Frederic Andersson > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Possible to constrain FDR to a label in the volume?
by Dan Dillon 02 Dec '08

02 Dec '08

Dear FreeSurfers, I've created a basal ganglia label and am wondering if it's possible to constrain the FDR calculation to that label? Based on earlier messages it seems like tksurfer has a "marked label only" option for FDR, but I haven't been able to find something similar in tkmedit. Any help greatly appreciated. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:dillon@wjh.harvard.edu> dillon(a)wjh.harvard.edu

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