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DirectoryLayout.txt
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Directory Layout:
/Volumes/Data/...
Is the location in which I store all large datasets and files. This includes
fMRI Experiment data and analyses, as well as Parallels* Virtual Machines.
fMRI data resides under the Exps Parent folder in one of two places. The Data
folder contains all raw and preprocessed data for the Experiments listed below
as well an Archive folder for failed Pilot projects )-`:
The Analysis folder contains GLM and higher level analysis for the listed
studies. This directory structure is linked to the Main Hagar drive so as
to allow Dianne to easily push data over without taking up space on the main
Hagar drive.
├── Exps
│ ├── Analysis
│ │ ├── HuanpingWB1
│ │ ├── Iceword
│ │ ├── Russian
│ │ ├── WordBoundary1
│ │ └── WordBoundary2
│ └── Data
│ ├── AttnMem
│ ├── Iceword
│ ├── Russian
│ ├── Stroop
│ ├── WordBoundary1
│ └── WordBoundary2
│ ├── Archive
│ │ ├── BehavStroop
│ │ ├── Dichotic
│ │ ├── Iceword_RealignDetails
│ │ ├── MLfMRI <-- Contains some papers on Machine Learning and fMRI
│ │ ├── MouseHunger
│ │ ├── RatPain
│ │ ├── TAP
│ │ ├── TBI
│ │ └── WB2
├── GlobalSession <-- This is where I store "Gloabal" afni files. Mainly Anatomicals
│ └── etc
│ └── Brains
├── Parallels
│ ├── Abel\ (1).pvm
│ │ ├── Abel-0.hdd
│ │ ├── Snapshots
│ │ └── Windows\ Disks
│ └── Ubuntu.pvm
│ ├── Snapshots
│ └── Ubuntu-0.hdd
└── WorkShop
------------------------------------------------------------------------------
/opt/local/...
Is the location where I keep all of my scripts. Every. Single. One. Want to
know what script I used for the Word Boundary1 GLM? Look under the WordBoundary
folder! I have done my best to organize scripts by project, so most times you should
only need to look under the Iceword folder for an Iceword specific program. Where that rule starts to break down is under the folder "WorkShop". This folder and its contents are a bit like the Wild Wild West. You are just as likely to find vast troves of knowledge as you are a breeding pit of vipers. If you want to see what my learning process was like, check in this directory.
Naming conventions tend to go as follows:
For later studies, such as WordBoundary, Iceword, and Russian I use 3 letter codes
to denote the experiment name, ie
WordBoundary1: wb1
WordBoundary2: wb2
Iceword: ice
Russian: rus
Preprocessing scripts are typically labelled in one of the following ways:
prep, preproc, pproc, pre, reg
GLM scripts are pretty consisitently labeled as:
glm
Group analysis scripts are often labeled as follows:
grp
Following that the naming conventions tend to focus on the type of task
involved. For example, if I am doing something involving SUMA focused, Ill
likely have "suma" in the file name.
So based on this naming convention, if you were looking for the Iceword
group analysis script I used to produce the group results, look under the
Iceword directory for a file called "ice.grp.sh". That would be your best
bet.
Some of the later studies, such as WordBoundary, Iceword, and Russian have
moderately well documented programs. For earlier stuff such as AttnMem, Stroop, Tap,
and Dichotic, it is a little less certain. My advice to you would be to look at what
and where the script is dumping files, and work backwards. ALL experimental data lives
under the /Volumes/Data/Exps/{Data,Analysis} directories. Obviously some of these
projects have moved machines over the years. Despite that, the basic file structure
should be fairly consistent with the actual experiment folder.
For example, Scripts belonging to the TAP expierment often point to the folder
/Volumes/Data/TAP. This is no longer the location of the TAP experiment data. However,
the layout of the directories under the TAP data folder have changed very little.
Let that be your guide....good luck! As an aside, you can find these scripts online at
https://github.com/KrbAlmryde/Utilities
I provide more indepth descriptions of what each folder actually contains, as well as some helpful hints as to which files are actually interesting or useful to look at. May it serve you well in the future.
├── Utilities
│ ├── AttnMem
│ ├── BootCamp
│ ├── Dichotic
│ ├── Iceword
│ ├── Modules
│ │ ├── GLMAnalysis
│ │ ├── Preprocessing
│ │ └── ShellScripting
│ ├── Mouse
│ ├── NBack
│ ├── NiftiViewer
│ ├── Rat
│ ├── Russian
│ │ ├── Event
│ │ └── Mixed
│ ├── Stroop
│ │ └── data
│ ├── SustainedAttention
│ ├── Tap
│ │ └── etc
│ ├── Tills
│ │ ├── Tests
│ │ └── excel_files
│ ├── WordBoundary
│ │ └── etc
│ ├── WordBoundary2
│ └── WorkShop
│ ├── AFNI
│ ├── AWK-SED
│ ├── PYTHON
│ ├── SHELL
│ └── etc