External Email - Use Caution Thanks a lot for the reply and the suggestions, Douglas! These scans are at 3T. Best, Darko
> ------------------------------ > > Message: 4 > Date: Wed, 20 Nov 2019 22:45:18 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Question about the input for longitudinal > processing pipeline > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <8be29ed9-8627-d005-fd9b-ca3ec56f8...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > 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 Komneni? 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 > > > > > >
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