nifti tools

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:

nii=load_nii(‘filename_with_hdr_extension’);
save_nii(nii, ‘desired_filename_for_niftifile.nii’);

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.

Then I read somewhere that we can actually create GIF images in command line mode using Imagemagick. But to do so you need to have Imagemagick installed on your system. To install it in Ubuntu, run:

sudo apt-get install imagemagick

This program has several features that would let you do all sorts of things with images. I was interested in converting a bunch of PNG files into an animated GIF file. To do so, we need to  rename the files in a way that they would lie in a sequence when arranged alphabetically (if you plan on doing it the easy way). Suppose you have files named slide_01.png, slide_02.png, slide_02.png….slide_xx.png, and you want to convert them to movie.gif, we run:

convert -delay 10 -loop 0 slide*.png movie.gif

The parameter delay inserts a desired delay between two consecutive slides. The number x used for delay inserts 10x milliseconds of delay between two frames. Loop parameter 0 makes it repeat infinitely.

If you had files with non-uniform names, then you need to input each of them in a sequence after the delay and loop parameters. Suppose you have file summer.jpg, fall, winter.jpg, fall.jpg and spring.jpg and you want to order them as fall, winter, spring and summer in the gif image seasons.gif with a 1 second delay between each of them, use:

convert -delay 100 -loop 0 fall.jpg winter.jpg spring.jpg summer.jpg seasons.gif

Here are some animations of numbers from 0 to 9 with varying delays.

The delay values specified the above cases were: 1, 5, 15, 25, 50 and 100.

GIF animation with 10 millisecond frame delay

GIF animation with 50 millisecond frame delay

GIF animation with 150 millisecond frame delay

GIF animation with 250 millisecond frame delay

GIF animation with 500 millisecond frame delay

GIF animation 1 second frame delay

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Photo iterations: or photo within photo

The picture looks quite interesting, as it depicts the same object at different time points within the same spatial space. I don’t see any artistic value in this picture, but what I do see is a lot of potential for philosophical discussion about time and space and how we can represent variations in time within a 2D space.