stowler

#!/bin/bash

# afniSwitchToRepo.sh
#
# A script to switch the user back to the neurodebian repo version of AFNI from a
# local alternative install (e.g., /opt/abin). Works in combination with
# afniSwitchFromRepo.sh

echo ""
echo "Switching back to the repo version of AFNI:"

stowler

#!/bin/bash

# afniSwitchFromRepo.sh
#
# A script to tempoarily switch the user from the neurodebian repo version of
# AFNI to a local alternative install (e.g., /opt/abin). Works in combination
# with afniSwitchToRepo.sh


# Specify the parent directory of alternative AFNI's binaries:

stowler

#!/bin/bash
#
# created: 20130724 by stowler@gmail.com
# edited:  20130724 by stowler@gmail.com
#
# This is a short script to illustrate quality control (qc) and conversion of
# Nocera CDA2 DICOM data.  
# - It is currently designed for FMRI runs from a single session of scanning
#   (i.e., one trip to the scanner, or one "study"). 
# - It is not written to accept commandline arguments. Instead, make a copy of

stowler

macula:OVF copy stowler-local$ diff -u Windows\ 7x86\ DanOrig.ovf Windows\ 7x86.ovf 
--- Windows 7x86 DanOrig.ovf  2013-07-16 17:15:35.000000000 -0400
+++ Windows 7x86.ovf	2013-07-17 12:10:02.000000000 -0400
@@ -54,14 +54,6 @@
         <vmw:Config ovf:required="false" vmw:key="ehciEnabled" vmw:value="true"/>
       </Item>
       <Item>
-        <rasd:Address>0</rasd:Address>
-        <rasd:Description>SCSI Controller</rasd:Description>
-        <rasd:ElementName>scsiController0</rasd:ElementName>

stowler

Mean proportion of negative bold voxels is greater in young group than oldOld group.

NB: polling only suprathreshold voxels where rsq > (.95 * participantRsqMax)

1. Significant (p=0.03) one-way ANOVA comparing group means of voxPropNeg:

---

 Df Sum Sq Mean Sq F value Pr(>F) 

stowler

setupNeuroimagingEnvironment.md

All of my scripts and documentation assume that these neuroimaging resources have been installed. For each package I cover the three computing environments I currently use:

• OS X Mountain Lion + MacPorts
• Neurodebian on Ubuntu 12.04 on 64-bit processors
• Neurodebian VM, running Debian 7.0 wheezy 32-bit on VirtualBox

Software covered:

stowler

#!/bin/bash

# scratch pad script for inital training with Jen
# stowler@gmail.com

# this is a short script to loop QA for Joe's data

seriesList="4 5 6 7 8 9"
parentDicomDir=~/Downloads/Fiji.app/DICOMSTORE/CDA101/MR/20130429/135538.453000/1
bxhDir=~/Downloads/bxh_xcede_tools-1.10.7-lsb30.x86_64/bin/

stowler

# stowler@gmail.com
# updated: 20130508
#
# These are my personal notes about installing neuroimaging software
# on Mac OS X Mountain/Lion and Ubuntu 12.04 (mostly neurodebian). 
#
# Some of this can be pasted into install scripts or the bash prompt.
# Be careful: this is an active working document, probably filled with errors.
#
# software covered:

stowler

#!/bin/bash
#
# workAround-installBxhOnMountainLion.sh
# stowler@gmail.com
#
# As of May 2013, the shipping version of BXH/XCEDE tools for OS X includes broken imagemagick:
#
#       $ bin/fmriqa_generate.pl ~/test.bxh ~/testQA
#       Trying int16 data type (instead of input uint16 datatype).
#       Checking for overflow...

stowler

$ bin/fmriqa_generate.pl ~/test.bxh ~/testQA
Trying int16 data type (instead of input uint16 datatype).
Checking for overflow...
dyld: Library not loaded: /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libclparser.dylib
  Referenced from: /Users/stowler/Downloads/bxh/bin/montage
  Reason: image not found
dyld: Library not loaded: /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libclparser.dylib
  Referenced from: /Users/stowler/Downloads/bxh/bin/convert
  Reason: image not found
...(snip)...