Greetings,
After successfully converting Afni files (full EPI's, statistical
functional images, Axial images, and mprage's) using fconvert, I am
having trouble during the alignment process. Before flirt, the 92
points of the 4-D EPI are preserved, as are the 2 sub-bricks of the
statistical functional image. After flirt, however, only one of the
sub-bricks seems to be kept (cannot toggle through in fslview) when
viewing it overlaid on the mprage.
Ultimately, the goal is to co-register the correct functional brick to
the mprage and then (possibly) move it back to Afni for talairach analysis.
Please pardon me if any of this is confusing or roundabout and thanks
for your time,
-Jeffrey O'Dell
Below are the automated commands used to attempt this:
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#!/bin/bash
## this script converts Afni MPRAGE, Ax, EPI and .fico files to Analyze
format
subj = x
ddate = y
mkdir "/data/mri/ANCfsl/S${subj}_${ddate}"
rm -rf "/data/mri/ANCfsl/S${subj}_${ddate}/"*
# MPRAGE 1st
echo "Converting MPRAGE to anz format..."
/usr/local/fiswidgets/tools/bin/fconvert -in afni -dir
"/data/mri/S${subj}_${ddate}" -file "S${subj}_${ddate}+orig.HEAD" -out
anz -dir "/data/mri/ANCfsl/S${subj}_${ddate}" -file "S${subj}_MPRAGE"
-datatype int16 -aux "glmin = 0, glmax = 4000"
echo "DONE Converting MPRAGE to anz format..."
echo "Fixing MPRAGE Orientation..."
avwswapdim "/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_MPRAGE" z -x -y
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_MPRAGEfd"
echo "Stripping MPRAGE Brain..."
/usr/local/fsl/bin/bet
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_MPRAGEfd"
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_MPRAGEfd_brain" -f 0.5 -g 0
# Axials 2nd
echo "Converting Axials to anz format..."
/usr/local/fiswidgets/tools/bin/fconvert -in afni -dir
"/data/mri/S${subj}_${ddate}Ax" -file "S${subj}_${ddate}_Ax+orig.HEAD"
-out anz -dir "/data/mri/ANCfsl/S${subj}_${ddate}" -file "S${subj}_Ax"
-datatype int16 -aux "glmin = 0, glmax = 4000"
echo "Fixing Axial Orientation..."
avwswapdim "/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_Ax" x -y z
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_Axfd"
echo "Stripping Axial Brain..."
/usr/local/fsl/bin/bet
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_Axfd"
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_Axfd_brain" -f 0.5 -g 0
# 1Hz raw (motion corrected) 3rd
echo "Converting 1 Hz raw (mc) AFNI to anz..."
/usr/local/fiswidgets/tools/bin/fconvert -in afni -dir
"/data/mri/S${subj}_${ddate}EPIs" -file
"S${subj}_${ddate}_1Hz_mc+orig.HEAD" -out anz -dir
"/data/mri/ANCfsl/S${subj}_${ddate}" -file "S${subj}_1Hz_mc" -datatype
int16 -aux "4d = true, glmin = 0, glmax = 4000"
echo "Fixing 1 Hz raw (mc) Orientation..."
avwswapdim "/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_1Hz_mc" x -y z
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_1Hz_mcfd"
echo "Stripping 1Hz raw (mc) Brain..."
/usr/local/fsl/bin/bet
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_1Hz_mcfd"
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_1Hz_mcfd_brain" -f 0.5 -g 0
# 1Hz fim 4th
echo "Converting 1 Hz fim (fico) AFNI to anz..."
/usr/local/fiswidgets/tools/bin/fconvert -in afni -dir
"/data/mri/S${subj}_${ddate}EPIs" -file
"S${subj}_${ddate}_1Hz_fim+orig.HEAD" -out anz -dir
"/data/mri/ANCfsl/S${subj}_${ddate}" -file "S${subj}_1Hz_fim" -datatype
int16 -aux "4d = true, glmin = 0, glmax = 4000"
echo "Fixing 1 Hz fim Orientation..."
avwswapdim "/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_1Hz_fim" x -y z
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_1Hz_fimfd"
# N.B. can't strip functional data - there's no brain or skull!
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#!/bin/bash
# 1) align EPI (motion corrected - "mc") to Ax, save EPI2Ax.mat (can't
extract EPI brain!)
# 2) align Ax to MPRAGE, save Ax2MPRAGE.mat
# 3) align fim to Axial using EPI2Ax.mat, save fim_reg2Ax.hdr
# 4) align fim_reg2Ax.hdr to MPRAGE using Ax2MPRAGE.mat, save
fim_reg2MPRAGE.hdr
subj=501
ddate=042603
# align EPI to Ax
#
echo "Aligning S${subj}_1Hz_mcfd_brain to S${subj}_Axfd_brain..."
flirt -in "/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_1Hz_mcfd_brain"
-ref "/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_Axfd_brain" -omat
"/data/mri/ANCfsl/S${subj}_${ddate}/EPI2Ax.mat" -out
"/data/mri/ANCfsl/S${subj}_${ddate}/1Hz_mc_reg2Ax" -dof 6
# align Ax to MPRAGE, save .mat and realigned Ax (Ax_reg2MPRAGE.hdr)
#
echo "Aligning S${subj}_${ddate}/S${subj}_Axfd_brain to
S${subj}_MPRAGEfd_brain..."
flirt -in "/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_Axfd_brain" -ref
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_MPRAGEfd_brain" -omat
"/data/mri/ANCfsl/S${subj}_${ddate}/Ax2MPRAGE.mat" -out
"/data/mri/ANCfsl/S${subj}_${ddate}/Ax_reg2MPRAGE" -dof 6
# align fim to Ax using EPI2Ax.mat
#
echo "Aligning S${subj}_1Hz_fimfd to S${subj}_Axfd_brain using EPI2Ax.mat"
flirt -in "/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_1Hz_fimfd" -ref
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_Axfd_brain" -applyxfm -init
"/data/mri/ANCfsl/S${subj}_${ddate}/EPI2Ax.mat" -out
"/data/mri/ANCfsl/S${subj}_${ddate}/fim_reg2Ax"
# align fim_reg2Ax.hdr to MPRAGE using Ax2MPRAGE.mat
#
echo "Aligning fim_reg2Ax to MPRAGEfd_brain using Ax2MPRAGE.mat"
flirt -in "/data/mri/ANCfsl/S${subj}_${ddate}/fim_reg2Ax" -ref
"/data/mri/ANCfsl/S${subj}_${ddate}/S${subj}_MPRAGEfd_brain" -applyxfm
-init "/data/mri/ANCfsl/S${subj}_${ddate}/Ax2MPRAGE.mat" -out
"/data/mri/ANCfsl/S${subj}_${ddate}/fim_reg2MPRAGE"
echo "Finished."
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Thanks if you read this far!
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