Dear list,
I have a question about dicom sorting and the coversion to nifti. That is, I used Osirix to sort dicom images into separate runs, and then use mri_convert to convert them from dicom to nifti, which works well for anatomical scans, but not for the functional ones. I have no clue what is lost in the funcitonal runs after sorting with Osirix.
So I tried with Dimon (afni) to sort, and 3DAFNItoNIFTI to convert, but the problem is, the functional and anatomical runs are all in the same folder,and Dimon seems to be a bit problematic with this,(Dimon searches for images that all have the same volume definitions,and since in one folder there are many different z-offset images)
Any suggestions will be helpful.
cheers, Jackie
Hi Jackie
what happens if you just use mri_convert from the start?
Bruce
On Wed, 4 Jul 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
I have a question about dicom sorting and the coversion to nifti. That is, I used Osirix to sort dicom images into separate runs, and then use mri_convert to convert them from dicom to nifti, which works well for anatomical scans, but not for the functional ones. I have no clue what is lost in the funcitonal runs after sorting with Osirix.
So I tried with Dimon (afni) to sort, and 3DAFNItoNIFTI to convert, but the problem is, the functional and anatomical runs are all in the same folder,and Dimon seems to be a bit problematic with this,(Dimon searches for images that all have the same volume definitions,and since in one folder there are many different z-offset images)
Any suggestions will be helpful.
cheers, Jackie _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The problem is likely osirix. It often strips off siemens-specific info needed to convert the mosaics that are used in the functionals. With mri_convert, you don't need to separate the dicom files into runs in separate directories, just pass it one dicom file from the run you want to convert, and it will figure everything else out.
doug
On Wed, 4 Jul 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
I have a question about dicom sorting and the coversion to nifti. That is, I used Osirix to sort dicom images into separate runs, and then use mri_convert to convert them from dicom to nifti, which works well for anatomical scans, but not for the functional ones. I have no clue what is lost in the funcitonal runs after sorting with Osirix.
So I tried with Dimon (afni) to sort, and 3DAFNItoNIFTI to convert, but the problem is, the functional and anatomical runs are all in the same folder,and Dimon seems to be a bit problematic with this,(Dimon searches for images that all have the same volume definitions,and since in one folder there are many different z-offset images)
Any suggestions will be helpful.
cheers, Jackie _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug ,
I've tried with this to sort, it did convert the dicom into nii, but I cannot tell this nii is build from which dicom images, and which image is the next input for mri_convert. Since in this folder, I got 2 functional and 2 anatomical scans, by looking at the serial numbers I cannot tell the acquisition time of these images, because they are not in a hierarchical order.
Any suggestions would be very helpful!
Cheers, Jackie
----- Original Message ----- From: Doug Greve greve@nmr.mgh.harvard.edu Date: Wednesday, July 4, 2007 6:37 pm Subject: Re: [Freesurfer] data conversion To: Chuan.Chih.Yang@rwth-aachen.de Cc: freesurfer@nmr.mgh.harvard.edu
The problem is likely osirix. It often strips off siemens-specific info needed to convert the mosaics that are used in the functionals. With mri_convert, you don't need to separate the dicom files into runs in separate directories, just pass it one dicom file from the run you want to convert, and it will figure everything else out.
doug
On Wed, 4 Jul 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
I have a question about dicom sorting and the coversion to nifti. That is, I used Osirix to sort dicom images into separate runs,
and then use mri_convert to convert them from dicom to nifti, which works well for anatomical scans, but not for the functional ones. I have no clue what is lost in the funcitonal runs after sorting with Osirix.>
So I tried with Dimon (afni) to sort, and 3DAFNItoNIFTI to convert, but the problem is, the functional and anatomical runs are all in
the same folder,and Dimon seems to be a bit problematic with this,(Dimon searches for images that all have the same volume definitions,and since in one folder there are many different z- offset images)
Any suggestions will be helpful.
cheers, Jackie _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thanks Doug!
I tried it out already and it works perfect!! (I could tell the order of the runs from the log) Plz forget my previous mail. :P
----- Original Message ----- From: Doug Greve greve@nmr.mgh.harvard.edu Date: Wednesday, July 4, 2007 6:37 pm Subject: Re: [Freesurfer] data conversion To: Chuan.Chih.Yang@rwth-aachen.de Cc: freesurfer@nmr.mgh.harvard.edu
The problem is likely osirix. It often strips off siemens-specific info needed to convert the mosaics that are used in the functionals. With mri_convert, you don't need to separate the dicom files into runs in separate directories, just pass it one dicom file from the run you want to convert, and it will figure everything else out.
doug
On Wed, 4 Jul 2007 Chuan.Chih.Yang@rwth-aachen.de wrote:
Dear list,
I have a question about dicom sorting and the coversion to nifti. That is, I used Osirix to sort dicom images into separate runs,
and then use mri_convert to convert them from dicom to nifti, which works well for anatomical scans, but not for the functional ones. I have no clue what is lost in the funcitonal runs after sorting with Osirix.>
So I tried with Dimon (afni) to sort, and 3DAFNItoNIFTI to convert, but the problem is, the functional and anatomical runs are all in
the same folder,and Dimon seems to be a bit problematic with this,(Dimon searches for images that all have the same volume definitions,and since in one folder there are many different z- offset images)
Any suggestions will be helpful.
cheers, Jackie _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Chuan.Chih.Yang＠rwth-aachen.de -
Doug Greve