Hello,
I have T1-weighted data from Philips 3 T scanner obtained at a resolution of 0.898 X 0.898 X 0.9 mm in both dicom (8 bit) and par/rec (pixel size = int16) format. I would like to preserve the acquisition resolution of the data in par/rec format; what is the best way to convert such data to mgz format for analysis in freesurfer? A command line example would be helpful, as I am new to freesurfer.
Thanks for your help,
Julie
Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676
I think you can just run mri_convert, passing it one dicom file from the series, eg
mri_convert one.dcm 001.mgz
this will preserve the resolution.
doug
Julie McEntee wrote:
Hello,
I have T1-weighted data from Philips 3 T scanner obtained at a resolution of 0.898 X 0.898 X 0.9 mm in both dicom (8 bit) and par/rec (pixel size = int16) format. I would like to preserve the acquisition resolution of the data in par/rec format; what is the best way to convert such data to mgz format for analysis in freesurfer? A command line example would be helpful, as I am new to freesurfer.
Thanks for your help,
Julie
Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Julie, The easiest way to preserve your data type would be to ask your Philips representative to switch DICOM export to 16 bit representation of the data. Alternatively, if you have access to an EasyVision console, you could try converting your .PAR/.REC into Analyze files with Philips' own tools. Otherwise, .PAR/.REC files deliver data in a flat format, so you could use the DICOMs to create a template volume in .mgh format, edit the datatype and attach the header to the .REC data (potentially swapping bytes and row ordering). This process is error prone though, and the .PAR/.REC-format is not well documented as far as I'm aware. Have you checked if your data actually use the 16 bits provided? Maybe you're not even losing anything. Cheers, Johannes
Am 17.11.2009 um 20:53 schrieb Julie McEntee:
Hello,
I have T1-weighted data from Philips 3 T scanner obtained at a resolution of 0.898 X 0.898 X 0.9 mm in both dicom (8 bit) and par/rec (pixel size = int16) format. I would like to preserve the acquisition resolution of the data in par/rec format; what is the best way to convert such data to mgz format for analysis in freesurfer? A command line example would be helpful, as I am new to freesurfer.
Thanks for your help,
Julie
Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Dr.med. Johannes C. Klein -
Julie McEntee