Convert between nii.gz and nii

[thomas.nickson]

Hey,

Are there any tools that can change between nii.gz and nii. I want to use some stuff that's in spm but I'd prefer to save space getting output in nii.gz where possible. Is there an intermediary that allows me to pipe in the nii.gz and nii out the other end to stick in the spm stuff?

Thanks,

Tom

[Michael Waskom]

I usually use the Freesurfer command mri_convert todo this (mri_convert foo.nii.gz foo.nii), which has a Nipype interface called MRIConvert.

But if you don't have Freesurfer installed, I'm sure there are other interfaces in Nipype that will do this, or you could just write a little Function interface that makes a system call to gunzip.

[Johnson, Hans J]

I think that the system call to unzip is the safest mechanism.  It would be lossless.  Convering with MRIConvert, or any of the other possible tools will only convert the parts of the nii.gz file that are known to that particular tool.

In particular, proprietary nifti extensions would be last.

With that stated, it “probably” does not affect you since your nifti files are “probably” simple and the conversions would be fine.

Hans

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[Cindee Madison]

This is a gzipped file

http://www.gzip.org/

gunzip <file> 

on most unix systems will work

to rezip

gzip <file>

--
Cindee Madison
Jagust Lab
UC Berkeley
cin...@berkeley.edu

[Cindee Madison]

and note...

The format is the same, just a matter of file compression

[thomas.nickson]

I think it's just a case of how to put this in to a pipeline easily though.

[Satrajit Ghosh]

hi tom,

nothing that does this automatically. a few options:

1. write a generic function that handles this case

2. gzip (create), gunzip (use):

http://www.mit.edu/~satra/nipype-nightly/devel/cmd_interface_devel.html#command-line-executable

https://github.com/nipy/nipype/blob/db81db1b5a5073d4e1e9793eb846fac4a1f476b5/nipype/algorithms/misc.py#L710 

3. add the functionality to the spm baseclass itself

4. (rare but they do exist in clusters) the filesystem hardware themselves do compression.

perhaps the gunzip from 2 is sufficient for your needs at this point.

cheers,

satra