Hi Mustafa
1. Your mprage ran through recon-all fine and the results look good. The
saggital field of view is tight, so make sure that they don't crop brain in
that direction.
2. Your recon-all command line is incorrect. You should point the
SUBJECTS_DIR environment variable to whereever you want to store all of
your FreeSurfer-processed data, then use the -i switch to path to the input
volume. You can also specify SUBJECTS_DIR on the command line. So in your
case something like:
recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 -sd \
/path/to/my/subjecs -all
should do the trick. There is also no need to convert to nifti first
cheers
Bruce
On Fri,
17 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
Herewith I attach within the email the command that didn't work when I wanted
to reconall. Please
have a look. What about the previous dicom that I have sent to you? Please
share some thoughts.Thank
you very much.
Yours faithfully,
Mustafa
Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
menulis:
Hi Mustafa
can you give us some detials? What didn't work? Can you send us the full
command line, screen output and recon-all.log?
cheers
Bruce
On Thu, 16 May 2019, mustafa amin wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> I tried to follow the instruction to recon-all the data however it didn't
work. Please give
> some thoughts. Thank you in advance.
>
> Yours faithfully,
>
> Mustafa
>
> Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu>
> menulis:
>
>
> Hi Mustafa, why not just run recon-all on the data you have and see
> whether it looks ok?
>
> On 4/15/19 7:06 AM, mustafa amin wrote:
> > External Email - Use Caution
> >
> > Hi Bruce,
> >
> > I’ve talked to the MRI operator and she told me that the best thing to do
the MP-RAGE
> protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set
the TE, TR, TI
> just like the ADNI protocol asked, though. She can set the thickness to 1 mm.
Is this set
> up okay?
> >
> > I have the DIACOM files of some subjects with the set up above. Can I send
them to you to
> look at them?
> >
> > I am terribly sorry for keep asking this basic question due to we never
had experience
> doing it in Indonesia.
> >
> > Many thanks!
> >
> >
> > Mustafa M. Amin
> > Consultant Psychiatrist in Biological Psychiatry
> > Department of Psychiatry
> > Faculty of Medicine
> > Universitas Sumatera Utara
> >
> >> On 2 Apr 2019, at 20.49, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
> >>
> >> Hi Mustafa
> >>
> >> MRI is an amazingly versatile technology that can be messed up in an
> >> astonishing number of ways. By far the best thing to do would be to acquire
> >> a dataset and run it through recon-all and see if the results look
> >> accurate. If you have permission to do so, you are welcome to acquire one
> >> and send it to us to try out instead.
> >>
> >> cheers
> >> Bruce
> >>
> >> On Tue, 2 Apr 2019, mustafa amin
> >> wrote:
> >>
> >>> External Email - Use Caution
> >>>
> >>> Dear Freesurfer experts,
> >>>
> >>> I need advice, the MRI operator need to confirm whether she had done the
> >>> right protocol of MP-RAGE. I have attached the picture that has been
> >>> taken by her. Please share some thoughts. Thank you in advance.
> >>>
> >>>
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>
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