[David Shattuck]

Hi Cristian –

How are you generating your .nii files in the first place? Do you have corresponding bvec and bval files already?

I don’t think we have a tool available from our site for doing this, but if you have FSL installed I believe you can do it with that. Let me know about the bvec/bval files, and I will see how we can help you with this.

thanks,
David Shattuck

[Cristianbio]

Hi David

Thanks for reply!

My .nii files are from DICOM files (from MRI dvd). I have converted dcm to nii because another tractography software requires .nii files. Yes, I have bvec and bval files.

Thanks,

Cristian

[David Shattuck]

Hi Cristian –

What tool did you use to convert them from DICOM to nifti? We typically use dcm2nii, which is included with MRIcron.

thanks,
David

[Cristianbio]

I have used 3DSlicer but dcm2nii sometimes too. In dcm2nii I have used “Modify nifti” option to convert .nii to .nii.gz but the tool convert one file at time, not all in one file.

Thanks,
Cristian

[Cristianbio]

Hi,

I resolved with dcm2nii, in particular with “NIFTI 3D -> 4D” option: with that, it create one .nii.gz file from multiple .nii files.

Thanks,

Cristian

[David Shattuck]

Hi Christian –

That’s great. One thing to make sure is that the order of the volumes is the same as is in your bvec/bval files. I’m not sure how best to do that. It might be safer to re-run dcm2nii on your original DICOM files, and make sure it outputs a 4D volume rather than individual 3D volumes. Are you using the latest version of dcm2nii?

We do have our own programs for merging DWI files (see here: http://neuroimage.usc.edu/neuro/Resources/BDPAddons#mergeDWIs), which is useful when a set of diffusion data is acquired as two different acquisitions. However, this program expects to have one bvec and one bval file per nii file. I think this would be different from how your data currently are stored.

thanks,
David

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