I got a skullstrippen mask from another pipeline to remove the noise in the MP2RAGE. Is it possible to give that to the recon-all? it is either a mnc or nii
thanks, mads On 5 October 2015 at 23:11, Andre van der Kouwe <an...@nmr.mgh.harvard.edu> wrote: > I think the standard MP2RAGE only generates the T1 image on the scanner. > With the Bloch simulation you can also figure out PD but the online > image analysis doesn't do it. > > On 10/05/2015 04:21 PM, Bruce Fischl wrote: >> I thought mp2rage lets you derive a proton-density (PD) weighted image, >> but I could be wrong. I'll cc Andre van der Kouwe who will know >> >> >> On Mon, 5 Oct 2015, Mads Jensen wrote: >> >>> Hi and thanks for the fast reply. >>> >>> Pardon my ignorance, but I am not sure that the PD images are? >>> >>> thanks, >>> mads >>> >>> On 5 October 2015 at 21:59, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>> wrote: >>>> Hi Mads >>>> >>>> my guess is that this is a problem with the MP2RAGE. We don't see >>>> this in >>>> the mprage or memprage. Can you look at the PD images in that region? Is >>>> the PD close to 0? Maybe you can threshold it out? That region is >>>> usually >>>> very dark on an mprage >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 5 Oct 2015, Mads Jensen wrote: >>>> >>>>> Hi, >>>>> >>>>> I got a problem with recon-all of T1's. The problem is that the >>>>> surfaces extent into what is essential noise, see linked images. The >>>>> problem is reoccurring in all the subjects I have ran so far, so I was >>>>> wondering if there could be a generic fix or if it will be necessary >>>>> to fix each recon individually. >>>>> >>>>> The sequence is a MP2RAGE recorded from a Siemens Skyra. >>>>> >>>>> thanks, >>>>> mads >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
