questions > dcm2nii using Nipype, change name of output
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Mar 10, 2017 02:03 PM | granitk
dcm2nii using Nipype, change name of output
The code that I have in Ipython is:
if ds.SeriesDescription == 'Ax_3D_T1w_BRAVO':
converter.inputs.output_dir = os.path.dirname(dir_3[MRrun])
converter.run()
This produces the output, but I want it also to change the name of the resulting .nii, for example, t1.nii.
Is this possible?
if ds.SeriesDescription == 'Ax_3D_T1w_BRAVO':
converter.inputs.output_dir = os.path.dirname(dir_3[MRrun])
converter.run()
This produces the output, but I want it also to change the name of the resulting .nii, for example, t1.nii.
Is this possible?
Mar 10, 2017 02:03 PM | Chris Rorden
RE: dcm2nii using Nipype, change name of output
Your choices will depend on the Python wrapper you are using
http://nipype.readthedocs.io/en/latest/i...
I would strongly recommend using the modern dcm2niix over dcm2nii. With dcm2niix you will want to specify the output filename parameter, e.g. "-f T1"
For more details, see the wiki
https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage
http://nipype.readthedocs.io/en/latest/i...
I would strongly recommend using the modern dcm2niix over dcm2nii. With dcm2niix you will want to specify the output filename parameter, e.g. "-f T1"
For more details, see the wiki
https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage
Mar 10, 2017 03:03 PM | granitk
RE: dcm2nii using Nipype, change name of output
Thousand thanx to you!
Where do I specify -f T1. Not in python i think :)
Where do I specify -f T1. Not in python i think :)
Mar 10, 2017 06:03 PM | granitk
RE: dcm2nii using Nipype, change name of output
Greatly appreciate an answer on this one
Mar 10, 2017 07:03 PM | granitk
RE: dcm2nii using Nipype, change name of output
I dont seem to be able to do the following: from
nipype.interfaces.dcm2nii import Dcm2niix
It says that it cannot import Dcm2niix. I have downloaded via Neurodebian and all is updated :/
It says that it cannot import Dcm2niix. I have downloaded via Neurodebian and all is updated :/
Mar 10, 2017 07:03 PM | Chris Rorden
RE: dcm2nii using Nipype, change name of output
Contact the Nipype team
https://github.com/nipy/nipype
https://github.com/nipy/nipype
Mar 11, 2017 06:03 PM | granitk
RE: dcm2nii using Nipype, change name of output
Its resolved! I hade to update Nipype. I got help via
neurostars.org.