nii2nii.gz

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    • #388
      Cristianbio
      Participant

      Hi all!

      I have a little problem.
      I have some .nii files for one subject: there is a tool to convert .nii files in one .noi.gz file? BDP require only one .nii.gz file for first step (in the terminal), so it see me an error and the process is halted.
      Thanks for help!

    • #390
      David Shattuck
      Keymaster

      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

    • #391
      Cristianbio
      Participant

      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

    • #392
      David Shattuck
      Keymaster

      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

    • #394
      Cristianbio
      Participant

      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

    • #436
      Cristianbio
      Participant

      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

    • #450
      David Shattuck
      Keymaster

      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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