In order to convert files in .img and .hdr format to a single .nii file, we first need to install the nifti tools toolbox for matlab.
Once the path for nifti tools has been set in matlab, the files in .hdr and .img format can be combined to create a .nii file by running the following two commands:
If you have freesurfer installed, you can convert between the files types with mri_convert by specifying the input (-it) and the output (-ot) type.
mri_convert -i name_of_input_file -it nifti1 -ot nii -o name_of_output_file
If you have functional dataset with several volumes over the course of your experiment, you can use the fslmerge function available in FSL to combine all the nifti files into a single 4D file.
fslmerge -t output_name.nii *.nii
Where *.nii would cover the entire set of nifti files if they are arranged sequentially.
Its not required to type in the extension .hdr or .img for the input image or output image if you have specified the input and the output types. By specifying the input type of nifti1, you tell the program that it will be a .hdr/.img pair, and specifying output type as nii goes for having your output with .nii extension.
To gzip the nifti file for use in freesurfer:
gzip filename.nii filename1.nii.gz
This will create a gzipped nifti file.
To automatically segment the structural volume:
recon_all -i filename1.nii.gz -subjid SUBJID -all
This will segment the structures containing in the structural file filename.nii.gz. Complete information on using recon-all for freesurfer can be found at FreeSurfer Wiki.
For some reason, Freesurfer seems to work well in tcsh. I’ve often encountered problems of weird nature when running it under bash. In order to run your autosegmentation with freesurfer type in tcsh at the terminal, since by default it is set to bash in most linux distros.