On 01/10/2016 12:20 PM, Andrea Bozoki wrote: > Plus, the > minute you take an ROI created by Freesurfer to analyze a PET image (which > cannot be surface-rendered accurately due to its inherent low resolution), > you are forced to ³translate² the borders of ROIs from FS to a > coordinate-based scheme anyway.
Not so fast. See for example Greve, et al, 2014. Cortical surface-based analysis reduces bias and variance in kinetic modeling of brain PET data > > I will try implementing your Freeview solution; thanks again. > > Andrea B. > > > On 1/9/16, 5:42 PM, "dgw" <dgwake...@gmail.com> wrote: > >> Hi Andrea, >> >> As far as I know no. >> >> Additionally, i don't think it makes a lot of sense to do, because the >> two parcellations are created in fsaverage space, and while there are >> morphings etc. that are possible these tricks will always introduce >> errors etc. Additionally MNI space is defined in a completely different >> way to Freesurfer space, and so translating the one two the other is >> strange, because in FS you have locations on a surface while in MNI they >> are 3d coordinates. Occasionally frustrating reviewers demand MNI >> coordinates, likely not realizing that in that translation they are >> being provided with strange data, and we have to send them something, >> but overall, I find that picking the atlas/space which makes sense for >> that question is the best place to start. >> >> hth >> d >> >> On 1/9/16 12:40 PM, Andrea Bozoki wrote: >>> Thank you. This is helpful. >>> >>> As to the broader question: is there truly no interactive, online atlas >>> that uses either the Destrieux or Duvernoy parcellation scheme to >>> examine >>> the landmark boundaries with respect to, say, MNI space? >>> >>> Thanks, >>> Andrea >>> >>> On 1/7/16, 4:26 PM, "dgw" <dgwake...@gmail.com> wrote: >>> >>>> freeview partial solution >>>> >>>> If this is important to you, you could write a quick script to do this >>>> for you: >>>> >>>> 1. mri_annotation2label to output all labels >>>> >>>> 2. write a script to launch freeview and load all of the labels >>>> (reading the color and applying it from the FS ctab file) >>>> >>>> e.g. freeview -f >>>> surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 & >>>> >>>> 3 you could then scroll through and click all of them off, and then >>>> click to load each one individually. >>>> >>>> or perhaps a new option could be added to the surface label called >>>> :label_opacity=0 (which would uncheck the view label option). >>>> >>>> hth >>>> d >>>> >>>> On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl >>>> <fis...@nmr.mgh.harvard.edu> >>>> wrote: >>>>> Hi Andrea >>>>> >>>>> I'm not sure what you mean but I'm pretty certain the answer is "no". >>>>> >>>>> sorry >>>>> Bruce >>>>> >>>>> On Thu, 7 Jan 2016, Andrea Bozoki wrote: >>>>> >>>>>> Is there any interactive or searchable version of the Destrieux atlas >>>>>> parcellations (the ones used by aparc.a2009s.annot)? >>>>>> >>>>>> It would be very helpful to be able to toggle back and forth between >>>>>> individual recon-all labels and a color atlas of the relevant region >>>>>> when >>>>>> examining ROI-based quantitative output (output that is not visual). >>>>>> >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Andrea B. >>>>>> >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> 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 >>> > > _______________________________________________ > 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 gr...@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
