Comments on: Converting .hdr/.img files to .nii

By: slash_boot

slash_boot — Wed, 09 May 2012 12:39:28 +0000

If you have freesurfer installed I would run the following script in terminal in the directory where you have your .nii files:
#!/bin/bash
for infiles in `ls *.nii`
do
fname=`echo $infiles | cut -d ‘.’ -f1`;
mri_convert $infiles -ot nifti1 $fname;
done

Now if you have a 4D image, and have FSL installed, things are even easier. Suppose your 4D file is named series.nii, run the following script at the terminal:

#!/bin/bash
export FSLOUTPUTTYPE=ANALYZE
fslsplit series.nii output_basename -t

Hope this helps!

By: Lena

Lena — Thu, 26 Apr 2012 11:03:50 +0000

Hi there,

I was wondering how do I convert nii files into their respective hdr and img files?

many thanks

By: slash_boot

slash_boot — Thu, 15 Sep 2011 13:27:00 +0000

You can use the .img file as the freesurfer input. Infact you can even get away without specifying the extensions.

By: tony

tony — Thu, 01 Sep 2011 00:58:53 +0000

If I want to use nifti hdr/img files as input, could you please tell me which of the following is right?

recon-all –i $FREESURFER_HOME/subjects/subj1/file.hdr –subject subj1 –all

recon-all –i $FREESURFER_HOME/subjects/subj1/file.img –subject subj1 –all

By: slash_boot

slash_boot — Mon, 11 Jul 2011 14:16:26 +0000

@Jared One option is to use mri_convert, which is a tiny program within freesurfer. If you have freesurfer installed, you can specify the output type as analyze.

By: Jared

Jared — Mon, 11 Jul 2011 13:58:59 +0000

Hey,
Does anyone here know how to do the opposite of this, that is, to convert .nii files to .img/.hdr analyze files?

By: Linda

Linda — Wed, 04 May 2011 16:20:25 +0000

You can either use load_nii(file_name, volume_range) to load data portion by portion, or simply use expand_nii_scan(file_name) to expand 4-D file to 3-D files, then use load_nii(3D_file_name).

By: Slashboot

Slashboot — Fri, 16 Jul 2010 20:33:35 +0000

If it is a 4-D file with lots of volumes, load_nii can run out of memory.

By: Qiuyun

Qiuyun — Fri, 16 Jul 2010 19:06:27 +0000

Does anybody have out of memory problem with load_nii?