Hi Martin, I am now trying to run it through the [CROSS] first, to see the effects. However, since our longitudinal data is already edited (i.e., in the base) i was interested to see if it was possible to pass the FLAIR in the longitudinal runs [LONG], which already have implemented the edited [BASE].
Best, Kasper 2016-05-17 14:59 GMT+02:00 Martin Reuter <mreu...@nmr.mgh.harvard.edu>: > Hi Kasper, > > if I remember correctly, you need to specify it in the cross and the long > runs (see my email below). Also could be you need the dev version, I have > never tested it in 5.3. > > Best, Martin > > > On 05/17/2016 03:54 AM, Kasper Jessen wrote: > > Unfortunately i do not think it works to pass it directly into a > longitudinal run. I tried the following, which exited with errors: > > recon-all -long d256a d256_base -FLAIR path/flair.nii.gz -autorecon3 > -FLAIRpial > > Any suggestions? > > Best, > > Kasper > > 2016-05-13 20:01 GMT+02:00 Martin Reuter <mreu...@nmr.mgh.harvard.edu>: > >> Hi Kasper, >> It should work (I tried it a while ago with the dev version and it did >> not crash :-). Could not really tell if it helped much either. >> I don't remember if functionality is available in FS5.3 to include that >> in a long run. In dev, you would include the T2 for both the cross and long >> run. The long run then takes the T2 from the cross. Not sure if it works >> passing it directly into a longitudinal run. >> >> Best, Martin >> >> >> On 05/13/2016 08:43 AM, Bruce Fischl wrote: >> >> Hi Kasper, >> >> I don't see why not, but we haven't done this yet I don't think, so there >> may be undiscovered bugs. >> Bruce >> On Fri, 13 May 2016, Kasper Jessen wrote: >> >> Dear FreeSurfer, >> Currently, we have only manual edited the BASE (the CROSS was left >> unedited) >> in an longitudinal data. However, some cortical areas (f.eks. such as the >> inferior temporal area) are difficult to edit accurately due to image >> quality. I then read through the release notes (stable v5.2.0) and found >> that a T2/FLAIR can be used to improve the pial surface. >> >> Question: Is it possible to use a T2 and run either -autorecon3 and >> -T2pial >> on the [LONG] runs to get extra improvement of the final pial surfaces? >> >> Best regards, >> Kasper Jessen >> >> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Martin Reuter, PhD >> Assistant Professor of Radiology, Harvard Medical School >> Assistant Professor of Neurology, Harvard Medical School >> A.A.Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Research Affiliate, CSAIL, MIT >> Phone: +1-617-724-5652 >> Web : http://reuter.mit.edu >> >> >> _______________________________________________ >> 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. >> >> > > > -- > Kasper Jessen, > MD, PhD student > Center for neuropsychiatric Schizophrenia Research (CNSR) > Mental Health Centre Glostrup > Nordre Ringvej 29-67 > 2600 Glostrup > Tlf.: 24430136 > E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > > > _______________________________________________ > 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. > > -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk
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