Dear Bruce,
I am a little confused and I will be very grateful if you can make it a little
more clear:
So I start converting the dicom files from 3DAx_T1 (having the first file
called 1.3.46.670589.11.17385.5.0.8952.2011042600464496394) series by running:
mri_convert 2011042600464496394.dcm 3DAx_T1.nii.gz (I suppose I need to
write only the last numbers). Then I am doing the same thing for all the dicom
files in this series?
After I finish the 3DAx_T1 I am moving further and do the same for all my
series?
Which series I shoul duse to run the recon-all for cortical thickness's studies?
Sorry for this silly question but for all my other subjects I had only one file
.nii.gz and I have no clue from where is coming.
Thank you very much.
Antonella
________________________________
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, July 21, 2011 11:08 AM
Subject: Re: dcm conversion to nii
Hi Antonella,
for each acquisition you give mri_convert *one* dicom file in that series
and it will figure out the rest. You will then have one volume file per
series. Something like:
mri_convert <one .dcm file in the Ax_PD series) Ax_PD.nii.gz
cheers
Bruce
On Thu, 21 Jul 2011, Antonella Kis wrote:
> Good morning Bruce,
>
> Thank you for your answer and yes, I am posting my question to the list.
>
> For all my other subjects I had the MRI data converted by somebody else into
> one file .nii.gz for each subject. My question is how I can
> convert the MRI data (.dcm) for a new subject in a .nii.gz file? I have
> multiple file from MRI: 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2,
> BOLD, DTI_15, DTI_32 each of them containing lots of .dcm files. Do I need to
> convert all of them? If I give mri_convert one slice in each
> dicom series and convert each one to it's own volume how I can further use
> this data? Do I get an .nii.gz for each dicom file?
>
> I attached a type of file .nii.gz from another subject so you can see what
> type of files I need to get by conversion.
>
> Thank you very much.
> Antonella
>
>
> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> To: Antonella Kis <ator...@yahoo.com>
> Sent: Wednesday, July 20, 2011 4:12 PM
> Subject: Re: dcm conversion to nii
>
> Hi Antonella
>
> can you post this type of question to the list so others can answer? I don't
> think you want them in one file as they probably have
> different resolution etc... Give mri_convert one slice in each dicom series
> and convert each one to it's own volume.
>
> cheers
> Bruce
> On Wed, 20 Jul 2011, Antonella Kis wrote:
>
> > Dear Bruce,
> >
> > I have the MRI data (.dcm) for my subject p27 within the following files:
> >
> > 3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, BOLD, DTI_15, DTI_32.
> >
> > I would like to convert this data into one file.nii.gz. It will be correct
> > if I will run:
> >
> > mri_convert p27 NPI027.nii.gz?
> >
> > Will FS know to convert based on this statement all my dcm files into one
> > nii.gz file? If not how should I do it?
> >
> >
> > Many thanks.
> > Antonella
> >
> >
> >
> >
> >
> >
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
