The conversion utility for PAR/REC data is now a Matlab script (or rather, a series of Matlab scripts). I've added these to everyone's Matlab path. If you have a custom startup.m you will need to addpath this directory: /afs/dbic.dartmouth.edu/usr/pkg/par_convert/par_convert
par_convert is able to output a variety of image formats (ANALYZE, AFNI, NIfTI) the default format is Analyze.
- Connect to rolando.cns.dartmouth.edu:
jed@dexter ~]$ ssh rolando.cns Dartmouth College, Department of Psychology and Brain Sciences Authorized access only firstname.lastname@example.org's password: Last login: Fri Jun 26 08:29:41 2009 from 126.96.36.199 [jed@rolando ~]$
- Navigate to your study directory and launch Matlab
[jed@rolando ~]$ cd /inbox/INTERA/dtiamyg/ [jed@rolando dtiamyg]$ matlab ... >>
- Execute par_convert function:
To convert an entire subject to AFNI format use the following syntax:
The conversion (and subsequent failure) of Sense Ref volumes will no longer be attempted.
>> par_boil('24feb09ro') Scan: 24feb09ro_01_1.PAR Modality: scout (Scout) Scan: 24feb09ro_02_1.PAR Modality: sense (Sense Ref) Scan: 24feb09ro_03_1.PAR Modality: mprage (Hi Res SENSE) Scan: 24feb09ro_04_1.PAR Modality: bold1 (fMRI_SSh SENSE) Scan: 24feb09ro_06_1.PAR Modality: dti (DTI_32_tensors SENSE) Scan: 24feb09ro_07_1.PAR Modality: bold2 (fMRI_SSh SENSE) Scan: 24feb09ro_10_1.PAR Modality: bold3 (fMRI_SSh SENSE) >> par_convert('24feb09ro','/tmp/24feb09ro') Writing data as: analyze Writing file: /tmp/24feb09ro/ANATOMY/scout Writing file: /tmp/24feb09ro/ANATOMY/mprage Writing file: /tmp/24feb09ro/FUNCTIONAL/bold1 volume:0001 Writing file: /tmp/24feb09ro/FUNCTIONAL/bold1 volume:0002 Writing file: /tmp/24feb09ro/FUNCTIONAL/bold1 volume:0003 Writing file: /tmp/24feb09ro/FUNCTIONAL/bold1 volume:0004 ... >>
The arguments are input directory and output directory. There is help available for all three of the functions (par_convert, r2a_convert, r2agui) The output directory is created for you if it doesn't exist. Your output directory will look just like our previous directories:
[jed at dbic-mrinbox 04may06dh]$ ls ANATOMY DTI FUNCTIONAL [jed at dbic-mrinbox 04may06dh]$ ls ANATOMY/ mprage.hdr mprage.img scout.hdr scout.img
The orientation will be the correct SPM/ANALYZE convention for the hires, coplanar, bold, and dti data. The scout isn't reorientated to save time.
Your functional data will be named with a 'bold' basename followed by the run number (starting with 1). The first volume will be named 'bold1_0001'. You will find these volumes in the FUNCTIONAL directory.
Your DTI data will also follow the above convention with a basename of 'dti1_0001' through 'dti1_0034'.
To convert a single PAR/REC file you can use the r2a_convert script. This script is called by the par_convert script (and uses the r2agui for all the heavy lifting).
>> help r2a_convert ... Usage: r2convert(parfile,subdir,modality) valid modality values: bold[n], mprage[n], coplanar[n], scout[n] >> r2a_convert('22apr06ac_3_1.PAR','/tmp','mprage'); Write file: /tmp/mprage
You will need to reorient these volumes yourself if you use r2a_convert manually. For our standard MPRAGE hires volume:
reorient mprage mprage xz o reorient mprage mprage yz o
For our standard EPI/BOLD data (note that you will need to do this for each volume you collect):
reorient bold1_0001 bold1_0001 y o reorient bold1_0001 bold1_0001 x o
If you have any problems with conversion or locating your data please contact me. The par_convert script may have trouble figuring out what is what if you do something slightly different. The basic logic is as follows:
- single volume, high slice count (>90) == hires
- single volume, real low slice count (<15) == scout
- single volume, mid slice count (>15 <90) == coplanar
- many volumes, bigger voxels (>2) == functional
- many volumes, smaller voxels(<2) == dti
This appears to do the job, but may need some tweaking.
All NIFTI-T1 files are stored in /inbox/NIFTI/YEAR/MONTH/DAY/SUBJECT. Example:
[jed@rolando]:/inbox/NIFTI/2012/10/31$ ls 24oct12hl
You can either use these directly or convert to your preferred format using any one of a number of utilities.