NIFTI files as input?

[Qingyang Li]

Dear all,

I have a question about CMP, does it accept NIFTI files as input? I read the online documentation and found no answer to my question... But with no Dicom files, CMP won't run?

Thanks!

Yang

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Qingyang Li

Balance and focus.

[Alessandra Griffa]

Dear Yang,

it is true that the CMP is thought to follow diffusion data processing from the Dicom files to the final result.
Anyway the Dicom step can be by-passed by copying your Nifti files in the NIFTI folder (T1.nii.gz; DSI.nii.gz or DTI.nii.gz or QBALL.nii.gz; eventually T2.nii.gz; eventually fMRI.nii.gz).

The DICOM converter step also saves the first volume of the diffusion dataset (NIFT/DSI_first.nii.gz or DTI_first.nii.gz or QBALL_first.nii.gz), and the first volume of the diffusion dataset resampled to 1x1x1 mm voxel size (Diffusion_b0_resampled.nii.gz). For this reason if you want to skip the DICOM converter step you should also provide these files.

Finally, before running each step the CMP is checking for the existence of at least one Dicom file in the RAWDATA/T1 and RAWDATA/diffusion folders. You can copy just one whatever Dicom file in each of these folders and skip the DICOM converter step.

Of course this process is tricky..
I'm going to release these days a new version of the CMP with easiest support for the Nifti.

Alessandra

[Qingyang Li]

Thank you very much, Alessandra, for the detailed reply.

I have another related question, I know CMP will check the orientation of the NIFTI images. I was wondering at what stage this orientation checking take place? During or after Dicom converter stage? If I do the trick as you suggested, will CMP check the orientation of the NIFTI files and reorient them as needed? or that's part of the Dicom converter stage? OK, this's not one question :D ...

Best,

Yang

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Qingyang Li

Balance and focus.

[cmpetty]

according to the log it happens in the DICOM -> NIFTI conversion:

INFO     : 2012-03-07 15:12:00,899 : main       : DICOM -> NIFTI conversion
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INFO     : 2012-03-07 15:12:34,540 : main       : Changing orientation /tmp/gene01/14059/NIFTI/T1.nii.gz to match /tmp/gene01/14059/NIFTI/DTI.nii.gz
INFO     : 2012-03-07 15:12:40,835 : main       : Input dataset has LPS orientation
INFO     : 2012-03-07 15:12:40,835 : main       : Reference dataset has LPS orientation
INFO     : 2012-03-07 15:12:40,835 : main       : No reorientation needed
INFO     : 2012-03-07 15:12:40,835 : main       : Module took 39.9366111755 seconds to process.