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]
>
> IMPORTANT WARNING: This email (and any attachments) is only intended for
> the use of the person or entity to which it is addressed, and may contain
> information that is privileged and confidential. You, the recipient, are
> obligated to maintain it in a safe, secure and confidential manner.
> Unauthorized redisclosure or failure to maintain confidentiality may
> subject you to federal and state penalties. If you are not the intended
> recipient, please immediately notify us by return email, and delete this
> message from your computer.
>
>
|