Apparently, the problem was in avwutils not working on the 4-d
dimension when flipping. The workaround was to use fconvert
under 3-D mode and to actively select the correct brick when
running flirt.
---- Original message ----
>Date: Fri, 8 Oct 2004 10:41:59 -0500
>From: "Jeffrey O'Dell" <[log in to unmask]>
>Subject: [FSL] Sub-brick lost after using flirt
>To: [log in to unmask]
>
>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:
>
>-----------------------------------------------------------------------
>
>#!/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!
>-----------------------------------------------------------------------
>
>-----------------------------------------------------------------------
>
>#!/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."
>-----------------------------------------------------------------------
>
>Thanks if you read this far!
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