-- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu From: "stdp82@virgilio.it" stdp82@virgilio.it Reply-To: "stdp82@virgilio.it" stdp82@virgilio.it Date: Tuesday, April 29, 2014 1:52 PM To: "Harms, Michael" mharms@wustl.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: R: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Hi Michael, please, see the file attached. They are reffered to FS and FSL visualization of the same file (R_thalamus overlapped on T1). Thanks, Stefano ----Messaggio originale---- Da: mharms@wustl.edu Data: 29-apr-2014 20.32 A: "stdp82@virgilio.it"stdp82@virgilio.it, "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Is the brain merely shown "sideways" in FSLview? What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have an RAS/LAS orientation. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu From: "stdp82@virgilio.it" stdp82@virgilio.it Reply-To: "stdp82@virgilio.it" stdp82@virgilio.it, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 29, 2014 1:19 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Hi Bruce, in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results. Thanks, Stefano ----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 29-apr-2014 17.52 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL How do you know the orientation is wrong? Is it right in tkmedit? On 04/29/2014 10:23 AM, stdp82@virgilio.it wrote: > My apologies, how can I visualize mri_binarize output? I tried in > fslview but orientation is wrong. Different orientation is a file's > feature or swapdim is request? > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: fischl@nmr.mgh.harvard.edu > Data: 29-apr-2014 16.01 > A: stdp82@virgilio.it, "Freesurfer support > list"freesurfer@nmr.mgh.harvard.edu > Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL > > Hi Stefano > > you can use either mri_binarize --match or mri_extract_label with labels > 10 and 49 (which I got from FreeSurferColorLUT.txt) > > cheers > Bruce > On Tue, 29 Apr 2014, > stdp82@virgilio.it wrote: > > > Hi list, > > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it > as seed > > mask in probtrackx. > > > > Thanks, > > > > > > Stefano > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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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