Thanks so much Matt - BrainVoyager files is exactly what I want to
convert.
Michael
On 25-Feb-09, at 10:29 AM, Matt Glasser wrote:
> Here is some code I used previously for this purpose:
>
> #!/usr/bin/env sh
>
> fslhd -x TT_avg152 > TT_avg152header.xml
> fslcreatehd TT_avg152header.xml blank
>
> while read line; do
> if echo $line | grep -q NrOfVOIs; then
> NrOfVOIs=`echo $line | awk '{ print $2 }'`
> echo got NrOfVOIs: $NrOfVOIs
> fi
> if echo $line | grep -q NameOfVOI; then
> NameOfVOI=`echo $line | sed -r 's/^.{11}(.*)$/\1/;s/
> /_/g;s/[^A-Za-z_]//g'`
> mkdir $NameOfVOI
> DirSTRING=`echo "$DirSTRING"" ""$NameOfVOI"`
> echo got NameOfVOI: $NameOfVOI
> fi
> if echo $line | grep -q NrOfVoxels; then
> NrOfVoxels=`echo $line | awk '{ print $2 }'`
> echo got NrOfVoxels: $NrOfVoxels
> fi
>
> Xmm=`echo $line | awk '{ print $1 }'`
> Ymm=`echo $line | awk '{ print $2 }'`
> Zmm=`echo $line | awk '{ print $3 }' | sed -r "s/[^0-9. -]//g"`
> if echo $Xmm | grep -qE '^[0-9.-]+$'; then
> Xvox=`echo "$Xmm * 0.5 + 45" | bc`
> Yvox=`echo "$Ymm * 0.5 + 63" | bc`
> Zvox=`echo "$Zmm * 0.5 + 36" | bc`
> Xr=`python -c "print int(round($Xvox))"`
> Yr=`python -c "print int(round($Yvox))"`
> Zr=`python -c "print int(round($Zvox))"`
> fslmaths blank -add 1 -roi $Xr 1 $Yr 1 $Zr 1 0 1 -bin
> "$NameOfVOI"/"$Xr"_"$Yr"_"$Zr"
> fi
> done < VOIs.voi
>
> for VOI in $DirSTRING ; do
> FilesSTRING=`ls "$VOI"/*.nii.gz`
> STRING=""
> for file in $FilesSTRING ; do
> STRING=`echo "$STRING"" -add ""$file"`
> done
> echo $STRING
> fslmaths blank $STRING $VOI
> done
>
> This was for converting some BrainVoyager VOI files to NIFTI files.
> The VOI
> files were basically text files with a bunch of coordinates and some
> header
> information. The most relevant lines for you are the two fslmaths
> lines
> where I first create a bunch of single voxel files and then add them
> together.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Michael Scheel
> Sent: Wednesday, February 25, 2009 12:23 PM
> To: [log in to unmask]
> Subject: Re: [FSL] import ROI through text file
>
> Hi, could you explain me how to use fslmaths to do this. I'm also
> still a matlab-beginner and if that's really easy to implement there
> I'd really appreciate some hints how to do it in matlab.
>
> Thanks, Michael
>
>
> On 25-Feb-09, at 12:47 AM, Steve Smith wrote:
>
>> Hi,
>>
>> If your ROI is specified via a textfile of coords then you could
>> script this with fslmaths but if your number of text voxels is huge
>> this could be slow. Alternatively it would be trivial in matlab and
>> then use save_avw to save to image file.
>>
>> Cheers.
>>
>>
>> On 25 Feb 2009, at 00:32, Michael Scheel wrote:
>>
>>> Hi everybody, is there a way to import an ROI into fsl and make a
>>> mask out of it.
>>> I have a textfile in 3 column format specifying the x y z of a
>>> number of voxels.
>>> I'd like to import this ROI and use it as a seed region for FDT.
>>>
>>> Thanks, Michael
>>>
>>
>>
>>
> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>
> ---------------------------------------------------------------------------
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