are there any downsides to running this script routinely on every diffusion
sequence?
cheers,
satra
On Wed, Feb 1, 2012 at 11:22 AM, Tyler Rolheiser <[log in to unmask]>wrote:
> I was having some trouble with the old rotbvecs script on a Mac (though
> not using CentOS), and this new version fixed it.
>
> Well done!
>
> Tyler
>
>
> On Wed, Feb 1, 2012 at 10:29 AM, Saad Jbabdi <[log in to unmask]> wrote:
>
>> Try this one.
>>
>> Saad
>>
>>
>>
>>
>>
>>
>>
>> On 1 Feb 2012, at 11:45, Sean F Walsh wrote:
>>
>> > Hi All,
>> >
>> > I am looking for some advice/help about rotating the gradient table for
>> diffusion data after eddy-current/motion correction. I downloaded the
>> rotate_bvecs script written by Martin Kavec. For some reason when I use
>> this script it always changes the final line in the new rotated bvecs file
>> into (0, 0, 0).
>> >
>> > The irritating thing is that the script used to work previously when I
>> ran it on a different computer - although I can't remember if we had to
>> change something first.
>> >
>> > I contacted Martin Kavec and he was helpful but unable to diagnose the
>> problem (and has apparently finished his scientific career).
>> >
>> > Any ideas on how I could go about fixing this?
>> >
>> > Please find the version of the script that I have at the end of this
>> message.
>> >
>> > Many thanks in advance,
>> >
>> > Sean
>> >
>> > #!/bin/bash
>> >
>> > if [[ $# -lt 3 ]] ; then
>> > echo "Incorrect Number of Paramaters Specified"
>> > echo "Usage: <original bvecs> <rotated bvecs> <ecclog> [-k]"
>> > echo ""
>> > echo "<ecclog> the output log file from ecc"
>> > echo "-k keep the mat files"
>> > echo ""
>> > exit 1;
>> > fi
>> >
>> > ECCLOG=$3;
>> > LIST="mat.list"
>> >
>> > if [ ! -e $1 ] ; then
>> > echo "Source bvecs $1 does not exist!"
>> > exit 1
>> > fi
>> >
>> >
>> > if [ -e $2 ] ; then
>> > echo "Target bvecs: $2 already exists!"
>> > exit 1
>> > fi
>> >
>> > if [ ! -e $ECCLOG ]; then
>> > echo "Ecc log file $3 does not exist!"
>> > exit 1
>> > fi
>> >
>> > if [ "$4" == "-k" ] ; then
>> > KEEP="YES"
>> > else
>> > KEEP="NO"
>> > fi
>> >
>> > ####################################################################
>> > # Create the mat files from input
>> > #
>> > # Here we read input ecclog file line by line, produce the FSL mat
>> > # file and fill it with respective trasformation. File listing all
>> > # the mat files generates is also created
>> >
>> > if [ -e ${LIST} ]
>> > then
>> > rm ${LIST}
>> > fi
>> >
>> > cat ${ECCLOG} | while read line; do
>> > #create a file name from processed volumes
>> > matfile=$(remove_ext $(echo ${line} | grep processing | awk '{print
>> $2}'));
>> > if [ "${matfile}" != "" ] ; then
>> > matfile=${matfile}.mat;
>> > echo "Generating ... ${matfile}";
>> > echo ${matfile} >> ${LIST};
>> > # following two reads will deal with unimportant lines
>> > read line;
>> > read line;
>> > # read matrix and store it in the current matfile
>> > read line;
>> > echo ${line} > ${matfile};
>> > read line;
>> > echo ${line} >> ${matfile};
>> > read line;
>> > echo ${line} >> ${matfile};
>> > read line;
>> > echo ${line} >> ${matfile};
>> > fi
>> > done
>> > #
>> > ####################################################################
>> >
>> > ####################################################################
>> > # rotate bvecs
>> >
>> > newXs="";
>> > newYs="";
>> > newZs=""
>> >
>> >
>> > BVECS=$1;
>> > Xs=$(cat $BVECS | head -1 | tail -1)
>> > Ys=$(cat $BVECS | head -2 | tail -1)
>> > Zs=$(cat $BVECS | head -3 | tail -1)
>> >
>> > MATs=$(cat mat.list);
>> >
>> > VOLUMES=$(cat $BVECS | head -1 | tail -1 | wc -w)
>> >
>> > if [ $VOLUMES != $(echo ${MATs} | wc -w) ]
>> > then
>> > echo "Number of *.mat files in $3 is not equal to number"
>> > echo "of gradients in $BVECS!"
>> > exit 1
>> > fi
>> >
>> > i=1
>> > while [ $i -le $VOLUMES ] ; do
>> > MAT=$(echo ${MATs} | cut -d " " -f ${i});
>> > #echo $MAT
>> >
>> > output=$(avscale --allparams ${MAT} | head -2 | tail -1)
>> > m11=$(echo $output | cut -d " " -f 1)
>> > m12=$(echo $output | cut -d " " -f 2)
>> > m13=$(echo $output | cut -d " " -f 3)
>> > m11=$(printf "%1.7f" $m11)
>> > m12=$(printf "%1.7f" $m12)
>> > m13=$(printf "%1.7f" $m13)
>> >
>> > output=$(avscale --allparams ${MAT} | head -3 | tail -1)
>> > m21=$(echo $output | cut -d " " -f 1)
>> > m22=$(echo $output | cut -d " " -f 2)
>> > m23=$(echo $output | cut -d " " -f 3)
>> > m21=$(printf "%1.7f" $m21)
>> > m22=$(printf "%1.7f" $m22)
>> > m23=$(printf "%1.7f" $m23)
>> >
>> > output=$(avscale --allparams ${MAT} | head -4 | tail -1)
>> > m31=$(echo $output | cut -d " " -f 1)
>> > m32=$(echo $output | cut -d " " -f 2)
>> > m33=$(echo $output | cut -d " " -f 3)
>> > m31=$(printf "%1.7f" $m31)
>> > m32=$(printf "%1.7f" $m32)
>> > m33=$(printf "%1.7f" $m33)
>> >
>> > X=$(echo $Xs | cut -d " " -f "$i")
>> > Y=$(echo $Ys | cut -d " " -f "$i")
>> > Z=$(echo $Zs | cut -d " " -f "$i")
>> > X=$(printf "%1.7f" $X)
>> > Y=$(printf "%1.7f" $Y)
>> > Z=$(printf "%1.7f" $Z)
>> >
>> > rX=$(echo "scale=7; ($m11 * $X) + ($m12 * $Y) + ($m13 * $Z)" |
>> bc -l);
>> > rY=$(echo "scale=7; ($m21 * $X) + ($m22 * $Y) + ($m23 * $Z)" |
>> bc -l);
>> > rZ=$(echo "scale=7; ($m31 * $X) + ($m32 * $Y) + ($m33 * $Z)" |
>> bc -l);
>> >
>> > rX=$(printf "%1.7f" $rX)
>> > rY=$(printf "%1.7f" $rY)
>> > rZ=$(printf "%1.7f" $rZ)
>> >
>> > # echo $rX" "$rY" "$rZ;
>> >
>> > rXs=${rXs}${rX}" ";
>> > rYs=${rYs}${rY}" ";
>> > rZs=${rZs}${rZ}" ";
>> >
>> > i=$(echo "$i + 1" | bc) ;
>> > done
>> >
>> > echo "$rXs" >> $2;
>> > echo "$rYs" >> $2;
>> > echo "$rZs" >> $2;
>> > #
>> > ####################################################################
>> >
>> > if [ "$KEEP" == "NO" ]; then
>> > rm $MATs $LIST
>> > fi
>> >
>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>>
>>
>>
>>
>>
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>>
>>
>
