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." <DGREVE@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: <d5205fe6-329a-f9b4-252a-8f1857aa42e4@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
>
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