Hi Matthew,
On 05/12/2010 09:51 AM, R. Matthew Hutchison wrote:
Hi group,
I am starting with Caret and have gone through most of the tutorials
using the data sets provided. The images are fantastic.
The part I seem to be missing is actually getting *my* activation maps
so that I can view them on the inflated surfaces.
If you use the menu 'Attributes', you'll find at the bottom 'Map
Volumes(s) to Surface'. I guess that is what you want. Took me a while
to find it as well ;-) .
I was wondering if anyone has a guide, steps, or hints in converting
the output files from FSL FEAT (registered to a standard atlas using
FSL FLIRT) to files viewable with Caret.
It seems this is not included in the tutorials.
T map macaque data of my individual monkeys to the caret F99 atlas, I
used FSL's FNIRT for a nonlinear transformation. Doing this once in a
way, that I was somehow satisfied with the result allows me to apply the
transformation on the statistical maps, if they are in the individual
monkey space. However, You might want to use the F99 atlas already as
standard template in the Feat analysis (if it yields convincing results).
I attached a small script that transforms a set of nii.gz-Nifti files
found within a directory into a new space according to a Flirt
transformation matrix file (linear) or a 3D volume with
warp-coefficients (Fnirt, nonlinear). Maybe this gives you an idea. I
cannot guarantee that it is bugfree, but at least It did work for me.
A search of the archive does not turn up any recent information on the
issue that I could find.
I am actually using macaque data but I figure the steps should be the
same as with the human but using the F99 atlas.
Perhaps I am just missing something obvious?
I understand that my data must be registered to the atlas space that I
wish to use in Caret.
But which FSL file should be used and what is the next step so that I
can view them?
If it is registered to the atlas then there should be no need to
segment the volumes again right?
You can use the zstat* images in the stats subdirecory of your copes as
statistical map that you transform to the standars F99 space. In this
case you can utilize the F99 segmentation, without segmenting the
individual brains. However, in my opinion you are loosing the
specificity of the localization, which in my view is one of the huge
advantages of primate fMRI. So I do both, mapping data on individual
brains, but also map all individuals on the standard atlas for comparision.
Thank you for any help (and patience for a novice),
I hope this gives you some pointers. Good luck anyway,
wolf
R.Matt Hutchison
--
R. Matthew Hutchison, PhD. Candidate
Centre for Functional and Metabolic Mapping
Robarts Research Institute
Cuddy Wing - 9.4T Suite
P.O. Box 5015, 100 Perth Drive
London, Ontario, Canada N6A 5K8
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#!/bin/bash
#
# batch_transform
#
# created: 19.02.2010
# by wolf
#
Usage() {
cat << EOF
Usage: $0 <trans_matrix> <ref_fl> [options]
transforms a list of functional volumes using a given
transformation matrix or warp coefficient volume
if the first argument is a transformation matrix, flirt will be used;
if it is a 3D volume file, fnirt is used.
OPTIONS:
-i input directory - use all files found in this directory
default is the current directory
-o output directory
-pf prefix
-sf suffix
-l use this list of files
-p search pattern for getting the list ('ls
*<pattern>*.nii.gz')
-thr lower threshold to be used after transformation
-f apply a threshold to functional data after transformation.
As default the minimum of original data is used as lower
thresshold.
-ip interpolation type. nn (default), trilinear, sinc, spline
(warp only)
-m create a transformed mask image in order to mask the data
###########################################################
## (c) wolf zinke (2010) - part of the MaFIA toolbox ##
## > MAcaque Functional Image Analysis < ##
## for comments and questions: [email protected] ##
###########################################################
EOF
exit 1
}
if [ $# -lt 2 ]; then
Usage
else
tmat=$1
refim=$2
shift 2
fi
#__________________________________________________________________________________________#
if [ ! -e $tmat ]
then
echo "ERROR: Transformation matrix not found!"
echo " file: $tmat"
exit
fi
if [ `imtest $tmat` -eq 1 ]
then
do_warp=1
ipstr='--interp=nn'
else
do_warp=0
ipstr='-interp nearestneighbour'
fi
if [ ! -e $refim ]
then
echo "ERROR: reference image not found!"
echo " file: $refim"
exit
fi
#__________________________________________________________________________________________#
odir=transformed
idir=`pwd`
get_list=1
prefix=''
suffix=''
get_thr=1
apply_thr=0
mask_img=0
pt=''
use_pt=0
while [ $# -gt 0 ] ;
do
case $1 in
-l) fllst=$2
get_list=0
shift 2
;;
-i) idir=`cleanpath $2`
shift 2
;;
-o) odir=`cleanpath $2`
shift 2
;;
-p) pt="$2"
use_pt=1
shift 2
;;
-sf) suffix=$2
shift 2
;;
-pf) prefix=$2
shift 2
;;
-thr) thr=$2
get_thr=0
apply_thr=1
shift 2
;;
-f) apply_thr=1
shift
;;
-ip)
if [ $do_warp -eq 1 ]
then
if [ $2 == 'nn' ]
then
ipstr='-interp nearestneighbour'
else
ipstr='-interp $2'
fi
else
ipstr='--interp=$2'
fi
shift 2
;;
-m) mask_img=1
shift
;;
-*) echo "Wrong option: <$1>"
echo ""
Usage
;;
*) break
;;
esac
done
#__________________________________________________________________________________________#
if [ $get_list -eq 1 ]
then
if [ $use_pt -eq 1 ]
then
fllst=""
for cpt in $pt
do
fllst="$fllst `ls -1 $idir/*.nii.gz | grep "$cpt"`"
done
else
fllst=`ls -1 $idir/*.nii.gz`
fi
fi
if [ ! -d $odir ]
then
mkdir $odir
fi
#__________________________________________________________________________________________#
for cfl in $fllst
do
flnm=`basename $cfl`
flnm=`remove_ext $flnm`
onm=`echo $odir/${prefix}${flnm}${suffix}`
if [ $do_warp -eq 0 ]
then
flirt -in $cfl -ref $refim -init $tmat $ipstr -applyxfm -out $onm
else
applywarp --ref=$refim --in=$cfl --out=$onm --warp=$tmat $ipstr
fi
if [ $(($mask_img + $get_thr)) -gt 0 ]
then
fslmaths $cfl -abs -bin tmp_cmask
fi
if [ $mask_img -eq 1 ]
then
if [ $do_warp -eq 0 ]
then
flirt -in tmp_cmask -ref $refim -init $tmat -applyxfm -out
tmp_cmask_trans
else
applywarp --ref=$refim --in=tmp_cmask --out=tmp_cmask_trans
--warp=$tmat $ipstr
fi
fslmaths tmp_cmask_trans -thr 0.25 -bin tmp_cmask_trans
fslmaths $onm -mas tmp_cmask_trans $onm
fi
if [ $apply_thr -eq 1 ]
then
if [ $get_thr -eq 1 ]
then
thr=`fslstats $cfl -k tmp_cmask -a -R | cut -d' ' -f1`
fi
fslmaths $onm -thr $thr $onm
fi
done
#__________________________________________________________________________________________#
if [ -e tmp_cmask.nii.gz ]
then
rm tmp_cmask.nii.gz
fi
if [ -e tmp_cmask_trans.nii.gz ]
then
rm tmp_cmask_trans.nii.gz
fi
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