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 fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@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.
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 fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@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 fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@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.
Hi Antonella,
no, you pick *one* file in each series (it doesn't matter which one, mri_convert will figure out the rest), and do something like:
mri_convert 1.3.46.670589.11.17385.5.0.8952.2011042600464496394.dcm 3DAx_T1.nii.gz
the only one(s) FreeSurfer will use are the 3D T1-weighted scans such as mp-rages. Those you will give to recon-all as inputs.
cheers Bruce
On Fri, 22 Jul 2011, Antonella Kis wrote:
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 fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@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 fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@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@nmr.mgh.harvard.edu
-
Antonella Kis -
Bruce Fischl