Hi-
We're doing structural imaging on a group of children (mean age 11 yr).
After finding that the adult priors/templates don't always produce the
right segmentation/standard space mapping results, we have tried to
switch to the Cincinnati Hospital's children brain templates. They have
T1 images and priors for grey/white matter and csf.
We found first that mfast didn't just work with these templates. The
templates are in MNI space, but their resolution is 1x1x1 mm^3 (rather
than the 2x2x2 mm^3 of the avg152* images). We were not sure that it was
because of this difference in size, the fact that one is big-endian and
one is little-endian or something else.
After mapping the T1 template of the Cincinnatti data to each of the
subject's data, applying that transformation to the priors, and naming
the transformed priors <sbjname>_prior_gm etc (mfast stopped when we
used <sbjname>_gm etc), it appears to have worked better. The next step
is using flirt to map the segmented images to the Cincinatti templates.
I'm not sure that the inner working of the script that we used (see
below) is the same procedure that would have happened if we had used the
avg152* templates and priors instead of our -Ap construction; i.e. are
those transformations the proper ones to use? If a FAST expert could
confirm that would be wonderful.
Thanks a lot
Alle Meije Wink
####################################################################
> #!/bin/bash
>
> PDFILES=`find $PWD/K* -name \*pd\*Axial\*masked.nii`
> PREFIX="$PWD/mediumchildren_9.6_12.9/kids"
>
> BRAINTEMP=`dirname ${PREFIX}`
> BRAINTEMP=${BRAINTEMP}/MaskedBrain.img
>
> for PDFILE in $PDFILES; do
>
> T2FILE=${PDFILE//pd/t2}
> PDDIR=`dirname $PDFILE`
>
> FSLOUTPUTTYPE="ANALYZE"
>
> echo "mapping template T1 to PD"
> COMMAND="flirt -in $BRAINTEMP -ref $PDFILE \
> -omat ${PDFILE//.nii/trans.txt}"
> echo "$COMMAND";$COMMAND
>
> echo "mapping priors"
> for TISSUE in _gm _wm _csf; do
> COMMAND="flirt \
> -in ${PREFIX}${TISSUE}.img -ref $PDFILE \
> -out ${PDFILE//.nii/_prior${TISSUE}.img} \
> -applyxfm -init ${PDFILE//.nii/trans.txt}"
> echo "$COMMAND";$COMMAND
> done
>
> COMMAND="mfast -s 2 -c 3 -i 50 \
> -A -Ap ${PDFILE//.nii/_prior} \
> -os -ob -or -op -ov $PDFILE $T2FILE"
> echo $COMMAND
> $COMMAND
>
> done
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