s0.updates.txt

2/1/15
======
s1.dataset
	- alias 'ls -l' problem fixed
	- added individual specifications for log_name and log_dir
	- if log_dir does not exist, script will put login home directory
	- log can now be put in $dest_dir, even if $dest_dir doesn't exist yet (it will be created)
	- added runs created to log, to keep a record of what has been created when
	- clean up

s2.make_spec
	- if log_dir does not exist, script will put login home directory

2/3/15
======
s3.task_surf_preproc && s3.task_surf_preproc
	- final run check will print runs processed and runs failed to log

2/17/15
=======
s1.dataset
	- changed format of date in log to 12 hour format
s2.make_spec
	- changed format of date in log to 12 hour format
s3.rest_surf_preproc
	- added x1D option to print a .1D of the design matrix
	- added quality check log
		- check # of censored TRs @ different thresholds
		- mean frame displacement
		- max displacement
		- will only write to quality check if currently being processed
		- quality check log will be appended to, processes as many times as you like, all will be kept

s3.task_surf_preproc && s3.task_surf_preproc
	- changed format of date in log to 12 hour format
	- script will print runs processed in current iteration properly to log
		(before it would print runs that already existed as processed, unless overwrite == yes)
	- cleaned up log file

2/22/15
=======
s3.rest_surf_preproc
	- made quality check optional
s3.task_surf_preproc
	- added quality check option as previously mentioned in s3.rest_surf_preproc
s3.rest_surf_preproc && s3.task_surf_preproc
	- added the option to only run quality check measures
		if overwrite == no and qual == yes, the script will only run quality check on runs that currently exist and are fully preprocessed, this way you can test certain censor limits quickly
	- script will now print runs that have already been processed to log, just so you know that it saw them and tagged them as already done
	- cleaned up documentation

2/24/15
=======
s3.rest_surf_preproc && s3.task_surf_preproc
	- fixed error in quality log
		before it would print the log title (with date) for each subject, now it only does it once

2/25/15
=======
s1.dataset
	- cleaned up script flow and log output
	- option to overwrite log
s2.make_spec
	- cleaned up script flow
	- option to overwrite log
s3.rest_surf_preproc && s3.task_surf_preproc
	- added ability overwrite log file
	- quality log removed and transferred to its own script (see below)
	- cleaned up output and script flow
s4.motion created (NEW SCRIPT)
	- this can: 
		show # of censored TRs @ different limits
		show mean/max displacement
		print enorm 1D file to visualize motion as a time series
		print separate censor files for the specified censor limits

3/10/15
=======
s1.dataset
	- script will tell you if the # of TRs in the run's dicom directory is different than the # you specified
	- script will print the names of failed runs to log

3/11/15
=======
s2.make_spec
	- The Successful @SUMA command reported in the log is no longer contingent solely on the creation of a SUMA directory.  
		In order for the command to be reported successful There needs to be a SUMA directory && 133 files within that directory (the number of files @SUMA_Make_Spec creates upon successful completion)
	- You can now specify a directory to move the SUMA directory to, script will check for its existence
	- added an overwrite option for the SUMA directory
all scripts
	- added a small section for known issues and features to be added later
s.update (NEW SCRIPT)
	- this will copy the newest versions of the scripts into either the present working directory or a specified path
	- usage takes either no arguments or a path argument, no argument goes to pwd, a path argument will copy to a specified path
	- it will prompt you to overwrite or not

3/13/15
=======
all scripts
	- clean up stout

3/15/15
=======
s.update
	- added individual script specifications
		specify one or more scripts to selectively update, or use -all to update all
	- added option -dir <directory>
		to specify a directory, if none is specified, scripts will be updated to pwd

3/17/15
=======
s3.task_vol_preproc (NEW SCRIPT)
	- volume preprocessing (took out motion quality)
s4.motion
	- added options to write demeaned and derivatives of motion
s3.task_surf_preproc
	- took out motion parameter options (use s4.motion)
s.update
	- added s3.task_vol_preproc

3/25/15
=======
s1.dataset
	- altered the \rm command to escape possible rm aliases
s2.make_spec
	- altered the \rm command to escape possible rm aliases
s3.task_vol_preproc
	- altered the \rm command to escape possible rm aliases
s3.rest_vol_preproc
	- altered the \rm command to escape possible rm aliases
	- changed volume registrations steps to reflect afni_proc (also as in s3.task_vol_preproc)
	- all epi datasets will be registered to same base
	- incorporated demeaned MoPar into script (instead of raw)
	- moved calculate motion regressors step to right before deconvolve
s4.motion
	- altered the \rm command to escape possible rm aliases

3/30/15
=======
s3.task_vol_preproc
	- created full brain mask of all epi runs
	- changed 3dmerge to 3dBlurInMask to only smooth within brain mask, voxels outside mask will be preserved

4/1/15
======
s5.decon (NEW SCRIPT)
	- originally written for the live reward task (will have to be altered for others)
	- choice between normal linear regression and beta series
s.update
	- added s5.decon option

4/29/15
=======
s3.task_surf_preproc
	- changed volreg step to match other scripts and afni_proc.py pipeline

5/20/15
=======
s1.dataset
	- can now deal with:
		- 2 conflicting t1 runs, move than 2 it will skip and print the conflict to log
		- multiple conflicting functional runs, it will choose the run that equals the # of volumes you specified in the preamble
		- if there are 2 functional runs with the correct # of dicoms, it will skip and note it in the log
	- now prints the user that ran the script to the log
	- updated documentation in preamble

5/21/15
=======
s2.make_spec
	- now prints the user that ran the script to the log
	- cleaned up documentation in preamble

5/22/15
=======
s3.task_vol_preproc
	- added option to specify which run and volume to register everything to, your choice will be printed in the log
	- added a quality check to skip over FullMask step if it already exists

5/26/16
=======
s3.task_vol_preproc
	- add clean_output option to remove all unneeded previous steps for a cleaner and smaller output
	- script will output which steps failed to the log
	- added option want_tsnr, this will give you a tsnr dataset based on pb02.volreg and a mean TSNR.out for each run

5/27/15
=======
s3.task_vol_preproc
	- change -1D_matrix filename to be consistent with what cat_matvec wants during the volreg step 
	- added skip_bad_motion where you can specify (for computational purposes) to skip runs with bad motion.  If skip_bad_motion = yes, you need to specify the limit in percentage and the censor limit parameters
	- cleaned up log output and documentation

5/28/15
=======
s3.task_vol_preproc
	- for skip_bad_motion = yes, percent TRs censored will also be output to log
s3.rest_surf_preproc
	- now prints the user that ran the script to the log
	- cleaned up log output
	- change -1D_matrix filename to be consistent with what cat_matvec wants during the volreg step 
	- took out -Xjpg from nuisance regression, not needed

6/1/15
======
s1.dataset
	- will skip runA and runB block if there are no identified runs
	- changed documentation in preamble to state that TR length must be given in seconds, also changed terminology from "number of volumes in a run" to "number of TRs in a run" ... not sure why I didn't do this originally
s3.task_surf_preproc
	- now prints the user that ran the script to the log
	- cleaned up log output and documentation
	- added skip_bad_motion where you can specify (for computational purposes) to skip runs with bad motion.  If skip_bad_motion = yes, you need to specify the limit in percentage and the censor limit parameters
	- for skip_bad_motion = yes, percent TRs censored will also be output to log
	- change -1D_matrix filename to be consistent with what cat_matvec wants during the volreg step 
	- added option want_tsnr, this will give you a tsnr dataset based on pb02.volreg and a mean TSNR.out for each run
	- script will output which steps failed to the log
s3.rest_surf_preproc
	- changed 1dBport for to bandpass all in one step during regression (takes a LOT longer but nuisance regression and bandpass is all done in one step, less interpolation)

6/2/15
======
s.update
	- added -h to show documentation of which scripts and options you can request
	- if no options are given, script will tell you and print the help documentation
	- added s5.decon to the scripts that can be requested
	- updated documentation in preamble

6/4/15
======
s1.dataset
	- added the ability to create freesurfer file structure and orig file for recon-all
	- added FROM_IMAGE to read slice timing from image, better for switching between multiband and classic
s3.task_col_preproc
	- added skip_slice option to skip slice time correction for multiband data
s3.task_surf_preproc
	- added skip_slice option to skip slice time correction for multiband data
s3.rest_surf_preproc
	- added skip_slice option to skip slice time correction for multiband data

6/5/15
======
s3.rest_surf_preproc
	-added 3dTproject for nuisance regression for faster processing speeds
	-removed jobs option in preamble because speed isn't an issue anymore

6/8/15
======
s5.decon
	- much less hard coded, more flexible for other studies

6/13/15
=======
s4.motion
	- added ow_log option (long overdue)
	- updated preamble
	- added overwrite option for output files (censor, enorm, demean, derv)

6/24/15
=======
s4.motion
	- added .csv output option
	- reordered some set variables in the preamble for clarity's sake
	- added set noclobber so it won't fail if a file doesn't exist for the log or csv

6/26/15
=======
s1.dataset
	- cleaned up log output
s2.make_spec
	- cleaned up log output
s3.(all)
	- cleaned up log output
s4.motion
	- fixed bugs relating to missing runs

7/15/15
=======
s3.(all)
	- added option $resolution to specify what resolution you want your functional data to be warped to
	- cleaned up skip_slice option, will check if the file exists first

7/23/15
=======
s1.dataset
	- added columns of dicom_hdr that you need for scan parameters

8/14/15
=======
s3.task_surf_preproc
	- script looks for the correct file after the smoothing step

6/26/15
=======
s1.dataset
	- uses t1_mpr to look for the T1 instead of t1 to prevent conflicts with run identifiers for functional runs

10/4/16
=======
s3.*_surf_preproc
	-change std.141 to std.60 - not sure why I hadn't changed this before...

10/10/16
========
s3.rest_vol_preproc
	- add tlrc normalization - not sure why this wasn't there before
s3.* 
	- remove the slice time specification and make the program read slice timing from image - you know, to be more flexible for multiband and not
	- this assumes that slice time is in the image
	- add -align_centers to pb02

10/14/16
========
s3.rest_vol_preproc
	- added a bunch of stuff that I should have had before
		bandpass properly
		align properly
		clean up some typos
		proper SUMA SurfVol alignment
s3.rest_surf_preproc
	- added multiple censor options

12/21/16
========
dl.data
	- added a custom PI option to grab data from other PIs from the fmri server
		default is Elizabeth Redcay

1/10/17
=======
dl.data
	- added '-opt' option to quickly change between 2 PIs and studies (for speed with TVI and RED studies)

2/16/17
=======
dl.data
	- removed '-perm' option and added chgrp to psyc-dscn-data and chmod to g+w
	- added chmod gu+w
	- added find $dir/$s -type d -exec chmod g+s {} \;
	- added different ending if there is an error
	- script will now display info and sleep for 5 seconds so that the user can review it
	- added check to see if subject's folder exists

2/20/17
=======
dl.data
	- removed failed script ending as it doesn't make much sense...
	- changed sleep to 2
	- print if the subjects data was downloaded (rough guess!)

2/28/17
=======
s1.dataset_ISSS
	- template script to make .nii files instead of HEAD/BRIK datasets
s3.task_vol_preproc_ISSS
	- begin proc script for ISSS data
	- removed skip_bad_motion because it was just taking up space
	
8/1/17
======
dl.data
	- added -scan so that user can designate which DICOM directory they want if the subject has more than one (e.g. cmnt or CHT)

10/29/18
========
s3.task_vol_preproc
	- removed -align_centers yes from align_epi_anat.py because it kept causing issues