mrInitRet performs several steps in sequence:
select/create directory tree
crop inplanes
load Efile header information about each functional scan
edit recon parameters
edit data analysis parameters
create Readme.txt file
extract tSeries from the P*.mag files
perform blocked analysis to compute correlation, amplitude, and
phase maps
Step by step instructions, assuming that you performing all of
the steps:
1. Run matlab
cd to the correct home directory; the one where your tSeries
will be written. This directory should be identified with the <sessioncode>,
e.g., d:\mri\091201c. Note that the raw data (Raw/Anatomy, Raw/Pfiles)
can be in a different directory, or even on a CD. You will have
the opportunity to specify where to find 'em.
2.Type mrInitRet at the matlab prompt.
Select the operations you want to perform (the rest of these
instructions assume that you have selected all of the steps).
OK.
3. Modify the home directory (where the tSeries will be written),
and the raw directory (where the Pfiles and Anatomy are located).
Accept. mrInitRet now checks that the directories are valid,
and makes the Inplane/Original/TSeries subdirectory tree
if necessary.
If the directories are invalid, the directory dialog box
will re-appear giving you the opportunity, for example, to
choose
a different
raw directory.
4. Crop the inplane anatomies. Click on one of the displayed
images. Select bouding rectangle by clicking twice, to include
the
parts of the brain that you're interested along with some skull
(including
at least part of the skull helps the alignment). Either Yes
to accept, No to redo the crop, or Cancel to abort the crop
operation
(note that if you cancel, mrInitRet will try to continue using
a pre-existing crop if there was one).
Locate vAnatomy, using the dialog box that comes up next. Or cancel
if there is no vAnatomy yet for this subject.
5. Enter the reconstruction parameters. Some of the information
in this dialog box, extracted from the Efiles, is displayed
only
for your information. The yellow fields are editable. Note that
the last three of these fields may be set differently for each
functional scan. Use the '>>' and '<<' buttons to
page through the scans. Use the 'Copy>>' button to copy
the displayed values to all of the subsequent scans.
Description: text string description of the scanning session
Subject: subject's name or initials (should be consistent with
directory name for the subject's volume anatomy).
Initial frames to discard: number of frames to dump at the beginning
of each scan to allow for magnetic saturation, etc.
Subsequent frames to keep: note that these two numbers added together
may not exceed the total number of frames but they may be less
than the total number of frames.
Slices: a 'list' (actually a vector) of numbers. Most of the time
this will be [1:nSlices] where nSlices is the number of inplane
anatomies. Slices will be a subset of the inplane slices when you
run the functionals with a subslice prescription.
6.Enter the data analysis parameters. This information can be
changed later when running mrLoadRet. The buttons work the
same as those
for the reconstruction parameters dialog.
Detrend flag options
0 no trend removal
1 highpass trend removal (default)
2 quartic removal
-1 linear trend removal
7. Fill out the Readme dialog.
Select one or more text files to append to the end of the Readme.txt
file. Or cancel.
