Also Bruce, Can I use this command line for the new version of freesurfer "
mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask
brainmask.mgz norm.mgz brain.mgz". Thanks
Pascal.
On Fri, Feb 3, 2017 at 2:47 PM, Pascal Goodman <mgoozg...@gmail.com> wrote:
> Thanks b
l
>
> yes, that is the right command line. I don't know if you will need more
> control points, but that helped a lot. -a specifies the intensity threshold
> above 110 and -g specifies the spatial gradient for the 1d normalization
>
> cheers
> Bruce
>
> On Fri, 3 Feb 2017, P
fis...@nmr.mgh.harvard.edu>
wrote:
> Hi Pascal
>
> you can put the
>
> mri_normalize -b 20
>
> line in a file, and use it as the expert options in recon-all to rerun
> autorecon2-cp and autorecon3 with it
>
>
> cheers
> Bruce
>
> On Fri, 3 Feb 2017, Pascal Goodman wrot
> HI Pascal
>
> I got significantly improved results using -b 20 on the mri_normalize
> command line. Note that this has to come after the mprage. I think you can
> do it with an expert options file with:
>
> mri_normalize -b 20
>
>
> cheers
> Bruce
>
> On F
ok at
>
>
> cheers
> Bruce
> On Fri, 3 Feb 2017, Pascal Goodman wrote:
>
> Thanks bruce. Do I upload the entire file? Also,where can I find the
>> link? Pascal
>>
>> On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> wrote:
ot;mri_normalize -b 20" > x.opts
>
> recon-all -s subjectID -autorecon2-cp -autorecon3 -expert x.opts
>
> or if you ware starting from scratch, use your command with the -expert
> x.opts
> stuff at the end
>
>
> cheers
> Bruce
>
> On Fri, 3 Feb 2017, Pas
20 and so will reset it. BTW: I used all the way up to -b
> 25 and things improved, so you might try that. At some point you will
> start eroding the gray/white boundary as you increase the -b threshold, but
> 25 looked ok to me
>
> Bruce
>
>
> On Fri, 3 Feb 2017, Pascal Go
thanks bruce for your response. You only answered question 4. :)
Cheers,
Pascal
On Mon, Feb 6, 2017 at 12:27 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> it should just be:
>
> mri_normalize -b 25
>
>
> On Mon, 6 Feb 2017, Pascal Goodman wrote:
>
&g
<fis...@nmr.mgh.harvard.edu>
wrote:
> Hi Pascal
>
> what are you trying to achieve? Internally we have multiple prior maps of
> this type, but I don't think we are setup for a user to supply a different
> one
>
> cheers
> Bruce
>
>
> On Fri, 3 Feb 2017, Pascal
Hello Freesurfer,
I do have a question. Can FS take probability maps of tissue segmentation
as prior?
Thanks,
Pascal
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The
atterns. There may be other interventions
> though - can you send us some examples of where things don't look accurate
> to you?
>
>
> cheers
> Bruce
>
>
> On Fri, 3 Feb 2017, Pascal Goodman wrote:
>
> Hello Bruce, Thanks for replying. I am trying find ways to i
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