Thanks everyone.This one answers my question.
Jennifer Bramen, Ph.D.
Assistant Research Neuroscientist
UCLA Center for Cognitive Neuroscience
Developmental Cognitive Neuroimaging
David Geffen School of Medicine at UCLA
635 Charles Young Drive South
Los Angeles, CA 90095-7332
Phone: (310)267-5116
Fax: (310)525-0865
Email: [log in to unmask]
Campus Mail Code 176919
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Brian Patenaude [[log in to unmask]]
Sent: 17 March 2009 10:20
To: [log in to unmask]
Subject: Re: [FSL] Using atlas regions as a mask
Hi,
The Harvard-Oxford designations are in
"${FSLDIR}/data/atlases/HarvardOxford-*.xml"
if you use fslsplit on the atlas to generate the individual structure
volumes, you cando the following to rename them all by their anatomical
name.
for i in vol*.nii.gz ; do
echo $i
f=`${FSLDIR}/bin/remove_ext $i`
label=`echo $f | sed 's/vol000//g' | sed 's/vol00//g'`
echo "The label is ${label}"
name=`cat ${FSLDIR}/data/atlases/HarvardOxford-Cortical.xml | grep
"index=\"${label}\"" | awk -F\> '{ print $2 }' | awk -F\< '{ print $1 }'
| sed 's/,/ /g' | awk -F\( '{ print $1 }' | sed 's/ /_/g' | sed
"s/\'//g"`
${FSLDIR}/bin/immv $i ${name}_prob_1mm_HarvOx
done
cheers,
Brian
> If you go to:
>
> fmri/atlases/HarvardOxford/HarvardOxford-combo-maxprob-thr25-2mm
>
> You will be able to see predefined rois masks which have already been set
> up in FSL. There are not actually labelled, so you will have to overlay
> them in FSL view to establish which roi masks correspond to which region
> of the brain.
>
> I am assuming that you want to use these for functional data, in which
> case case you input these rois (one at a time) when you perform your
> higher level FEAT analyses. Here you are confining the thresholding to a
> particular region (e.g., left ACC). FEAT will ignore all voxel outside the
> roi mask. In post-stats, you input the roi mask where is says
> "pre-threshold masking".
>
> Perhaps there are other methods you can use, but perhaps give this one a
> go.
>
> Liam.
>
>
> *******************************************
> Liam Nestor, Ph.D
> Office C8-523
> Laboratory for Molecular Neuroimaging
> Semel Institute for Neuroscience and Human Behavior
> 760 Westwood Plaza
> Los Angeles 90024
> Tel: 310-206-0655
> E-mail: [log in to unmask]
> *******************************************
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of
> Teena Moody [[log in to unmask]]
> Sent: Tuesday, March 17, 2009 9:40 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Using atlas regions as a mask
>
> Jen,
> Ashley, Jesse and I have some ROIs already made for several regions
> from the MNI 25 and 50% atlases. We probably have slightly different
> methods, I will try to send you notes that Ashley sent me. I forward
> an old email if i can find it.
> Teena
> On Mar 16, 2009, at 2:07 PM, Jennifer Bramen wrote:
>
>> Dear FSL List
>>
>> I would like to use individual regions of interest from one of the
>> free atlases. However, the
>> atlases are composed of multiple regions and I do not know how to
>> create a separate mask
>> for an individual region. Is there a command I can use?
>>
>> Thanks
>>
>> jen
>
> Teena Moody
> [log in to unmask]
>
>> Semel Institute at UCLA
>> 760 Westwood Blvd. Suite B8-169
>> Los Angeles, CA 90095
>> (310) 794-9360 lab
>> (310)503-5630 cell
>> [log in to unmask]
>
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