Hoffman2:Scripts:gen movie.py - Revision history

Hwang: /* Setup Environment */

2024-08-27T23:01:03Z

Setup Environment

← Older revision		Revision as of 23:01, 27 August 2024
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	conda activate /u/project/CCN/apps/conda/rh7/ccn_py37		conda activate /u/project/CCN/apps/conda/rh7/ccn_py37
	module load ffmpeg/5.0.1		module load ffmpeg/5.0.1

			If you want to run this script on other Linux machines instead of Hoffman2, make sure you have Python3, Nibabel and ffmpeg installed.

	==Usage/Help==		==Usage/Help==

Melodie: /* Example */

2024-08-27T15:22:42Z

Example

← Older revision		Revision as of 15:22, 27 August 2024
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	==Example==		==Example==

	/u/project/~~ccn~~/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100 --dim 2		/u/project/CCN/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100 --dim 2

	In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.		In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.

Hwang: /* Usage/Help */

2024-08-26T22:46:24Z

Usage/Help

← Older revision		Revision as of 22:46, 26 August 2024
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	Output directory for movie file		Output directory for movie file
	-d DIM, --dim DIM Create movie with specific dimension, i.e. options: 0 or 1 or 2. defaul: 2		-d DIM, --dim DIM Create movie with specific dimension, i.e. options: 0 or 1 or 2. defaul: 2
			0: Sag 1: Cor 2: Axial
	-b BIN, --bin BIN Number of bins used in histogram. i.e. 100		-b BIN, --bin BIN Number of bins used in histogram. i.e. 100
	-w WIN, --win WIN Window range. i.e. "0.05 0.995"		-w WIN, --win WIN Window range. i.e. "0.05 0.995"

Hwang: /* Example */

2024-08-26T22:39:43Z

Example

← Older revision		Revision as of 22:39, 26 August 2024
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	==Example==		==Example==

	/u/project/ccn/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100		/u/project/ccn/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100 --dim 2

	In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.		In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.

Hwang: /* Usage/Help */

2024-08-26T22:39:26Z

Usage/Help

← Older revision		Revision as of 22:39, 26 August 2024
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	-o OUTDIR, --outdir OUTDIR		-o OUTDIR, --outdir OUTDIR
	Output directory for movie file		Output directory for movie file
			-d DIM, --dim DIM Create movie with specific dimension, i.e. options: 0 or 1 or 2. defaul: 2
	-d DIM, --dim DIM Create movie with specific dimension, i.e. defaul: 2

	-b BIN, --bin BIN Number of bins used in histogram. i.e. 100		-b BIN, --bin BIN Number of bins used in histogram. i.e. 100

	-w WIN, --win WIN Window range. i.e. "0.05 0.995"		-w WIN, --win WIN Window range. i.e. "0.05 0.995"

Hwang: /* Usage/Help */

2024-08-26T22:38:45Z

Usage/Help

← Older revision		Revision as of 22:38, 26 August 2024
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	-o OUTDIR, --outdir OUTDIR		-o OUTDIR, --outdir OUTDIR
	Output directory for movie file		Output directory for movie file

			-d DIM, --dim DIM Create movie with specific dimension, i.e. defaul: 2

	-b BIN, --bin BIN Number of bins used in histogram. i.e. 100		-b BIN, --bin BIN Number of bins used in histogram. i.e. 100

	-w WIN, --win WIN Window range. i.e. "0.05 0.995"		-w WIN, --win WIN Window range. i.e. "0.05 0.995"

Hwang: /* Example: */

2024-08-16T01:49:26Z

Example:

← Older revision		Revision as of 01:49, 16 August 2024
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	-w WIN, --win WIN Window range. i.e. "0.05 0.995"		-w WIN, --win WIN Window range. i.e. "0.05 0.995"

	==Example:==		==Example==

	/u/project/ccn/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100		/u/project/ccn/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100

Hwang: /* Example: */

2024-08-16T01:40:49Z

Example:

← Older revision		Revision as of 01:40, 16 August 2024
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	In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.		In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.

	Also in this case, the script will apply a histogram with 100 bins, the data value lower than 0.05 or higher than 0.995 will be replaced by windowing method.		Also in this case, the script will apply a histogram with 100 bins on the MRI data, the data value lower than 0.05 or higher than 0.995 will be replaced by windowing method.
			The window range and numbers of bins can be adjusted with --win and --bin options.

Hwang: /* Example: */

2024-08-16T01:39:36Z

Example:

← Older revision		Revision as of 01:39, 16 August 2024
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	/u/project/ccn/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100		/u/project/ccn/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100

	In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.		In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.

			Also in this case, the script will apply a histogram with 100 bins, the data value lower than 0.05 or higher than 0.995 will be replaced by windowing method.

Hwang at 01:32, 16 August 2024

2024-08-16T01:32:44Z

← Older revision		Revision as of 01:32, 16 August 2024
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	-w WIN, --win WIN Window range. i.e. "0.05 0.995"		-w WIN, --win WIN Window range. i.e. "0.05 0.995"

	Example:		==Example:==

	/u/project/ccn/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100		/u/project/ccn/apps/scripts/gen_movie.py -i /path/to/T1w_brain.nii.gz -o /path/to/output/ --win "0.05 0.995" --bin 100

	In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.		In this example, the script will read the input file from /path/to/T1w_brain.nii.gz and create a "movie" folder under /path/to/output/ and generate a movie file from the input file under movie/ folder, named as mri_movie.mp4. So you will find the output file at /path/to/output/movie/mri_movie.mp4.