questions > dcm2niix convert to 4D and output dir issue
Showing 1-2 of 2 posts
Sep 16, 2016 11:09 PM | Nina de Lacy
dcm2niix convert to 4D and output dir issue
Hi there:
New user of dcm2niix here. I installed MRIcroGL, running dcm2niix from the command line on Mac (El Cap). Am using to convert data acquired on a Philips 3T -- 3D structural and resting state. Here is the syntax I used:
dcm2niix -o "Users/username/blah/moreblah/NIFTI_subdirectory" -z n /Users/username/blah/moreblah/DICOM_filename_for_individual_image
The conversion ran, but I experienced the following:
1. Couldn't find my output directory
2. Converted all my dicoms, instead of a single one
3. Gave me individual volumes for the resting state
I am wondering what I'm doing wrong with specifying the output directory, how to specify a single file if desired, and if there is an option to concatenate the volumes for the resting state in to 4D during conversion or if I need to do 3D to 4D file conversion as a separate step.
Thanks very much,
Nina de Lacy
New user of dcm2niix here. I installed MRIcroGL, running dcm2niix from the command line on Mac (El Cap). Am using to convert data acquired on a Philips 3T -- 3D structural and resting state. Here is the syntax I used:
dcm2niix -o "Users/username/blah/moreblah/NIFTI_subdirectory" -z n /Users/username/blah/moreblah/DICOM_filename_for_individual_image
The conversion ran, but I experienced the following:
1. Couldn't find my output directory
2. Converted all my dicoms, instead of a single one
3. Gave me individual volumes for the resting state
I am wondering what I'm doing wrong with specifying the output directory, how to specify a single file if desired, and if there is an option to concatenate the volumes for the resting state in to 4D during conversion or if I need to do 3D to 4D file conversion as a separate step.
Thanks very much,
Nina de Lacy
Sep 21, 2016 06:09 PM | Chris Rorden
RE: dcm2niix convert to 4D and output dir issue
Thanks for sending me sample images, these look really nice. With
my software you use the option "-s y" to convert a single file,
otherwise it will convert all the images in the specified folder.
This behavior is nice for most DICOM images where the 3D volumes
and 4D time series are saved as thousands of individual files each
with a 2D image. Your Philips system has bundled all the slices
from each series as a single file, so you may prefer the "-s y"
option to explicitly control which image is converted.