On Tue, Jan 22, 2013 at 4:06 AM, "Falk Lüsebrink" <falk.luese@gmx.net> wrote:

Hey Dan,

Bruce might be right about the SNR, but you could try to adjust the parameters of the inhomogeneity correction in the N3 algorithm.

You could either use the following command line:
recon-all -autorecon1 -mprage -nuintensitycor-3t -i <data> -s <subject>

Or if this still isn't good enough, try changing the parameters of the N3 manually (e.g. distance and fwhm):
SUBJ=ab11

recon-all -motioncor -talairach -tal-check -i <data> -s $SUBJ

mri_nu_correct.mni --i $SUBJECTS_DIR/$SUBJ/mri/orig.mgz --o $SUBJECTS_DIR/$SUBJ/mri/nu.mgz --proto-iters 1000 --distance 15 --fwhm 0.5 --n 1 --uchar $SUBJECTS_DIR/$SUBJ/mri/transforms/talairach.xfm

recon-all -mprage -normalization -skulstrip -s $SUBJ

If the skullstrip looks fine continue by using this:
recon-all -mprage -autorecon2 -autorecon3 -s $SUBJ

Best,
Falk

-------- Original-Nachricht --------
> Datum: Mon, 21 Jan 2013 22:39:29 -0500
> Von: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> An: Dan LaFreniere <lafreniere.dj@gmail.com>
> CC: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Betreff: Re: [Freesurfer] Trouble with Initial Processing - Very Dark Images

> Wow, that's a huge bias field! Control points will help uniformity, but
> the snr may not be good enough for good results
> Bruce
>
>
>
> On Jan 18, 2013, at 11:09 AM, Dan LaFreniere <lafreniere.dj@gmail.com>
> wrote:
>
> > Hey all,
> >
> > I'm very new to Freesurfer and am having some issues with the initial
> processing of our MPRAGE dicom files. So far, I'm able to get initial
> -autorecon1 steps to work but once this has finished and I open my brainmask.mgz
> files and the brain is incredibly dark in inferior regions. So much so that
> the skull strip appears to be removing large chunks of anterior temporal
> lobes. What remains of the temporal lobes is incredibly dark with grey matter
> almost indistinguishable from CSF.
> >
> > I would really like to look into freesurfer for cortical thickness
> analysis of subcortical regions since it seems like such an awesome program but
> I have really been struggling to get a decent looking brain. It's probably
> noteworthy that these brains have always been quite dark but I'm usually
> able to correct them to a point where they're pretty good in other programs.
> >
> > I have read about a few solutions to the problem but am having trouble
> implementing them. One suggestion was to use the -mprage flag;
> unfortunately, I'm not sure how to run this or when. Another suggestion was to use
> control points but I don't yet have the red and blue segmentation boundary lines
> - I'm using tkmedit FoM04_KA brainmask.mgz -aux T1.mgz to view the files.
> For reference, this is the line I use to run autorecon1: Recon-all
> -autorecon1 -subjid FoM04_KA
> >
> > Does anyone have any suggestions as to what I could do? It would be
> greatly appreciated. I've attached a screenshot to illustrate. Also, we used a
> 4.7T Varian scanner with 0.375/0.375/1mm voxels. I believe we used a
> gradient echo multislice sequence. In addition, all subjects' data have been
> obtained so there is no chance of changing sequences…
> >
> > Best wishes,
> >
> > Dan

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