BASH Tricks - Revision history

Chris: /* Make a series of numbered directories */

2022-09-27T19:57:26Z

Make a series of numbered directories

← Older revision		Revision as of 15:57, 27 September 2022
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	''Protip:'' If you want to also make the <code>runs</code> file that some of our scripts use at the same time, the above snippet can be modified:		''Protip:'' If you want to also make the <code>runs</code> file that some of our scripts use at the same time, the above snippet can be modified:
	for i in $(seq -f "%03g" 1 6); do mkdir ${i}; echo ${i} >> runs; done		for i in $(seq -f "%03g" 1 6); do mkdir ${i}; echo ${i} >> runs; done

			=== Save list of numbered directories to file ===
			Another protip: If you already had a set of numbered directories and want to save them to a list (e.g., a "runs" file):
			while read s; do
			ls "$SUBJECTS_DIR/$s/bold" \| grep "^00*" > $SUBJECTS_DIR/$s/bold/runs
			done <subjects

	== Restart Window Manager ==		== Restart Window Manager ==

Chris at 01:11, 6 July 2021

2021-07-06T01:11:10Z

← Older revision		Revision as of 21:11, 5 July 2021
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			==Text File Batch==
			Suppose we have a list of items to process -- like all the entries in the <span style="color:red;">subjects</span> file, for example. We want to use each line in the file in a for-loop:
			while read s; do
			echo "$s";
			done <<span style="color:red;">subjects</span>

	== How many lines in my text file? ==		== How many lines in my text file? ==
	Totally useful when you have some kind of training file with many rows and columns:		Totally useful when you have some kind of training file with many rows and columns:

Chris: /* Making a tar archive containing only the minimal set of structural files for FreeSurfer */

2020-09-28T14:28:36Z

Making a tar archive containing only the minimal set of structural files for FreeSurfer

← Older revision		Revision as of 10:28, 28 September 2020
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	== Making a <code>tar</code> archive containing only the minimal set of structural files for FreeSurfer ==		== Making a <code>tar</code> archive containing only the minimal set of structural files for FreeSurfer ==
	FreeSurfer makes a zillion files during the recon-all step. I have no idea what most of them are there for. Which do we need? The absolute minimal list is a work in progress, but I have made a file called '''fsaverage.required''' (copied to /ubfs/caset/cpmcnorg/Scripts/fsaverage.required) based on the contents of the fsaverage template subject directory contents. I dropped the obvious directories (e.g., mri 2mm), so what's left should hopefully be close to the minimal required set for getting things done with a subject. The idea is to reduce the number of superfluous files that you store or copy over the network so that we don't waste as much time and disk space with useless nonsense.		FreeSurfer makes a zillion files during the recon-all step. I have no idea what most of them are there for. Which do we need? The absolute minimal list is a work in progress, but I have made a file called '''fsaverage.required''' (copied to <code>/ubfs/caset/cpmcnorg/Scripts/fsaverage.required</code>) based on the contents of the fsaverage template subject directory contents. I dropped the obvious directories (e.g., mri 2mm), so what's left should hopefully be close to the minimal required set for getting things done with a subject. The idea is to reduce the number of superfluous files that you store or copy over the network so that we don't waste as much time and disk space with useless nonsense.

	So here's what you do (note the text in red will vary - don't just blindly copy the code snippets below and expect them to work; that's how Chernobyl happens! You need to understand what you're doing):		So here's what you do (note the text in red will vary - don't just blindly copy the code snippets below and expect them to work; that's how Chernobyl happens! You need to understand what you're doing):

Chris: /* Making a tar archive containing only the minimal set of structural files for FreeSurfer */

2020-09-28T14:28:09Z

Making a tar archive containing only the minimal set of structural files for FreeSurfer

← Older revision		Revision as of 10:28, 28 September 2020
Line 28:		Line 28:

	== Making a <code>tar</code> archive containing only the minimal set of structural files for FreeSurfer ==		== Making a <code>tar</code> archive containing only the minimal set of structural files for FreeSurfer ==
	FreeSurfer makes a zillion files during the recon-all step. I have no idea what most of them are there for. Which do we need? The absolute minimal list is a work in progress, but I have made a file called '''fsaverage.required''' (copied to ~~the~~ ubfs ~~scripts directory~~) based on the contents of the fsaverage template subject directory contents. I dropped the obvious directories (e.g., mri 2mm), so what's left should hopefully be close to the minimal required set for getting things done with a subject. The idea is to reduce the number of superfluous files that you store or copy over the network so that we don't waste as much time and disk space with useless nonsense.		FreeSurfer makes a zillion files during the recon-all step. I have no idea what most of them are there for. Which do we need? The absolute minimal list is a work in progress, but I have made a file called '''fsaverage.required''' (copied to /ubfs/caset/cpmcnorg/Scripts/fsaverage.required) based on the contents of the fsaverage template subject directory contents. I dropped the obvious directories (e.g., mri 2mm), so what's left should hopefully be close to the minimal required set for getting things done with a subject. The idea is to reduce the number of superfluous files that you store or copy over the network so that we don't waste as much time and disk space with useless nonsense.

	So here's what you do (note the text in red will vary - don't just blindly copy the code snippets below and expect them to work; that's how Chernobyl happens! You need to understand what you're doing):		So here's what you do (note the text in red will vary - don't just blindly copy the code snippets below and expect them to work; that's how Chernobyl happens! You need to understand what you're doing):

Chris: /* What directories are in one directory but not the other? */

2020-04-03T17:55:06Z