External Email - Use Caution        

Hi Bruce,

Thank you for your swift response as always, may I know how to convert the more than 100 DICOM files to mgz or nifti? I noticed that the command is for 1 file/image, please correct me if I am wrong. The MP-RAGE file that I sent you is more than 50 images.

I tried to follow your instruction however it did not work smoothly. The diacom files couldn't be converted to mgz. I have attached the command that still did not work when I used them in this email. Please have a look and share some thoughts. Thank you for your kind attention and cooperation.


Pada Jumat, 17 Mei 2019 21.14.44 WIB, Bruce Fischl <fischl@nmr.mgh.harvard.edu> menulis:


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 <fischl@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. <DGREVE@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 <fischl@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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