I have not run images with contrast, but I think it should work. Some people have tried to use the mp2rage UNI scan, but it often fails because of very bright voxels outside of the brain. If you can remove those (eg, skull stripping), then it might work. Alternatively, if you have a quantitative T1 that comes out of the mp2rage if you have the license, then you can simulate an mp1rage that will then work in FS (but it will have bias fields). If you don't have a qT1, it is not too hard to convert the UNI to qT1. Is this at 3T or 7t?
On 11/19/19 5:35 AM, Darko Komnenić wrote: > > External Email - Use Caution > > Hi Douglas, > thanks for your reply. Indeed, in this particular data set they don't > all have contrast, which is unfortunate. But my question was also > general, if we assume that they all have contrast, would it be OK to > use those images as inputs in the longitudinal pipeline? And the same > question for mp2rage images, are they OK to use as well, or are they > not suitable for this pipeline? > Best, > Darko > > > ------------------------------ > > Message: 11 > Date: Mon, 18 Nov 2019 18:41:37 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>> > Subject: Re: [Freesurfer] Question about the input for longitudinal > processing pipeline > To: "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa4...@mgh.harvard.edu > <mailto:d5205fe6-329a-f9b4-252a-8f1857aa4...@mgh.harvard.edu>> > Content-Type: text/plain; charset="utf-8" > > Do all images and time points have contrast? If some do and some > don't, > then I don't think you can properly do the analysis? > > On 11/15/19 10:06 AM, Darko Komneni? wrote: > > > > ????????External Email - Use Caution > > > > Dear Freesurfer experts, > > I wanted to run the Freesurfer's longitudinal processing pipeline > > (described here > > > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) > on a > > series of MRI scans from a single patient. However, after > looking at > > the scans, i realized that for most time points, the patient > doesn't > > have a "simple/normal" T1 MPRAGE sequence available. Instead, they > > have a T1 sequence with a contrast agent, as well as T1 mp2rage > > sequences. > > > > Is it possible/advisable to run recon-all in general or this > pipeline > > in particular on T1 MPRAGE scans that have a contrast agent, or > that > > are mp2rage instead of MPRAGE? > > > > Thanks in advance! > > Best, > > Darko > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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
