Extracting CLUT from .annot Files Using R - Revision history

Chris: /* clutteR.R */

2020-03-31T16:12:40Z

clutteR.R

← Older revision		Revision as of 12:12, 31 March 2020
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	2 "G_and_S_occipital_inf" 23 60 180 0		2 "G_and_S_occipital_inf" 23 60 180 0

	So after you generate your CLUT.txt file, you might want to use <code>sed</code> to strip the quotation marks.		So after you generate your CLUT.txt file, you might want to use <code>sed</code> to strip the quotation marks:
			sed -i .bak 's/\"//g' lh.a2009s-CLUT.txt
			Note: the '''-i .bak''' flag tells sed to run the command in-place (i.e., overwriting the original), but saving a back-up with the .bak extension. This is the MacOS syntax. I believe linux syntax differs, so you can run <code>man sed</code> to see what options are available on your OS.

Chris: /* clutteR.R */

2020-03-31T16:05:55Z

clutteR.R

← Older revision		Revision as of 12:05, 31 March 2020
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	./clutteR.R lh.aparc.a2009s.annot lh.a2009s-CLUT.txt		./clutteR.R lh.aparc.a2009s.annot lh.a2009s-CLUT.txt
	If an outfile is not specified, the outputfile will be the name of the input file with -CLUT.txt appended to it.		If an outfile is not specified, the outputfile will be the name of the input file with -CLUT.txt appended to it.

			My one complaint with this script is that R writes strings with quotation marks:
			"#No." "Label Name" "R" "G" "B" "A"
			0 "Unknown" 0 0 0 0
			1 "G_and_S_frontomargin" 23 220 60 0
			2 "G_and_S_occipital_inf" 23 60 180 0

			So after you generate your CLUT.txt file, you might want to use <code>sed</code> to strip the quotation marks.

Chris: /* freesurferformats */

2020-03-31T15:40:05Z

freesurferformats

← Older revision		Revision as of 11:40, 31 March 2020
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	=freesurferformats=		=freesurferformats=
	There are at least two R packages written to work with FreeSurfer files. The freesurferformats package has utilities to pull the CLUT from a .annot file		There are at least two R packages written to work with FreeSurfer files. The [https://cran.r-project.org/web/packages/freesurferformats/index.html freesurferformats package] has utilities to pull the CLUT from a .annot file
	==Installing freesurferformats==		==Installing freesurferformats==
	In R:		In R:

Chris: /* freesurferformats */

2020-03-31T15:39:34Z

freesurferformats

← Older revision		Revision as of 11:39, 31 March 2020
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	=freesurferformats=		=freesurferformats=
	There are at least two R packages written to work with FreeSurfer files. The ~~freesurferfileformat~~ package has utilities to pull the CLUT from a .annot file		There are at least two R packages written to work with FreeSurfer files. The freesurferformats package has utilities to pull the CLUT from a .annot file
	==Installing freesurferformats==		==Installing freesurferformats==
	In R:		In R:

Chris: Created page with "=freesurferformats= There are at least two R packages written to work with FreeSurfer files. The freesurferfileformat package has utilities to pull the CLUT from a .annot file..."

2020-03-31T15:38:13Z

Created page with "=freesurferformats= There are at least two R packages written to work with FreeSurfer files. The freesurferfileformat package has utilities to pull the CLUT from a .annot file..."

New page

=freesurferformats=
There are at least two R packages written to work with FreeSurfer files. The freesurferfileformat package has utilities to pull the CLUT from a .annot file
==Installing freesurferformats==
In R:
install.packages('freesurferformats', dependencies=TRUE)

=Reading .annot files=
With the package installed, you can now read .annot file information:
library('freesurferformats')
annotfile='lh.aparc.annot'
annot=read.fs.annot(annotfile)
colortable=colortable.from.annot(annot)

=Scripting=
You can run an R script from the terminal using the Rscript shell interpreter by beginning your script with the following:
#!/usr/local/bin/Rscript

Write the rest of your script using normal R syntax. Save it with a .R extension and make it executable and you can run it from the terminal. You can even pass parameters:
#!/usr/local/bin/Rscript
args = commandArgs(trailingOnly=TRUE)
print(args[1]) #this prints the first argument

=clutteR.R=
I learned all this this morning, and wrote an R script to extract the CLUT from a .annot file. The script, clutteR.R can be found in the /ubfs/Scripts/R folder. Run it as follows:
./clutteR.R annot-file [outfile]

For example:
./clutteR.R lh.aparc.a2009s.annot lh.a2009s-CLUT.txt
If an outfile is not specified, the outputfile will be the name of the input file with -CLUT.txt appended to it.