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CoBrALab / atlases

Segmentations of Neuroanatomy on Hi-Res T1 and T2 MRIs and publicly available population averages in MNI space
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Add nifti versions of the atlases and FSL compatible XML #3

Open chrisgorgo opened 8 years ago

chrisgorgo commented 8 years ago

A Nifti version of the atlases together with an FSL compatible XML file describing the labels would greatly improve the usefulness of this resource!

gdevenyi commented 8 years ago

Some nifti versions are available here http://cobralab.ca/atlases/

Can you provide a pointer to the FSL xml docs? We don't use FSL so we don't have any experience with that.

There will soon be a refresh and re-release of atlases/labels to support MAGeT v2 I'm working with.

pipitone commented 8 years ago

It's quite simple: specification here. For example: 

<!-- JHU-labels.xml -->
<?xml version="1.0" encoding="ISO-8859-1"?>
<atlas version="1.0">
  <header>
    <name>JHU ICBM-DTI-81 White-Matter Labels</name>
    <type>Label</type>
    <images>
      <imagefile>/JHU/JHU-ICBM-labels-1mm</imagefile>
      <summaryimagefile>/JHU/JHU-ICBM-labels-1mm</summaryimagefile>
    </images>
    <images>
      <imagefile>/JHU/JHU-ICBM-labels-2mm</imagefile>
      <summaryimagefile>/JHU/JHU-ICBM-labels-2mm</summaryimagefile>
    </images>
  </header>
  <data>
<label index="0" x="0" y="0" z="0">Unclassified</label>
<label index="1" x="69" y="83" z="36">Middle cerebellar peduncle</label>
<label index="2" x="89" y="97" z="40">Pontine crossing tract (a part of MCP)</label>
<label index="3" x="93" y="152" z="77">Genu of corpus callosum</label>
<label index="4" x="95" y="100" z="97">Body of corpus callosum</label>
<label index="5" x="85" y="89" z="88">Splenium of corpus callosum</label>
<label index="6" x="89" y="116" z="88">Fornix (column and body of fornix)</label>
<label index="7" x="82" y="103" z="43">Corticospinal tract R</label>
<label index="8" x="97" y="103" z="43">Corticospinal tract L</label>
<label index="9" x="84" y="89" z="40">Medial lemniscus R</label>
<label index="10" x="95" y="89" z="40">Medial lemniscus L</label>
<label index="11" x="83" y="83" z="20">Inferior cerebellar peduncle R  </label>
<label index="12" x="96" y="83" z="20">Inferior cerebellar peduncle L</label>
<label index="13" x="84" y="93" z="53">Superior cerebellar peduncle R</label>
<label index="14" x="95" y="93" z="53">Superior cerebellar peduncle L</label>
<label index="15" x="75" y="107" z="60">Cerebral peduncle R</label>
<label index="16" x="104" y="107" z="60">Cerebral peduncle L</label>
<label index="17" x="75" y="129" z="79">Anterior limb of internal capsule R</label>
<label index="18" x="104" y="129" z="79">Anterior limb of internal capsule L</label>
<label index="19" x="66" y="108" z="85">Posterior limb of internal capsule R</label>
<label index="20" x="113" y="108" z="85">Posterior limb of internal capsule L</label>
<label index="21" x="61" y="101" z="78">Retrolenticular part of internal capsule R</label>
<label index="22" x="117" y="101" z="78">Retrolenticular part of internal capsule L</label>
<label index="23" x="69" y="163" z="73">Anterior corona radiata R</label>
<label index="24" x="110" y="163" z="73">Anterior corona radiata L</label>
<label index="25" x="63" y="109" z="96">Superior corona radiata R</label>
<label index="26" x="116" y="109" z="96">Superior corona radiata L</label>
<label index="27" x="64" y="99" z="99">Posterior corona radiata R</label>
<label index="28" x="115" y="99" z="99">Posterior corona radiata L</label>
<label index="29" x="57" y="64" z="73">Posterior thalamic radiation (include optic radiation) R</label>
<label index="30" x="122" y="64" z="73">Posterior thalamic radiation (include optic radiation) L</label>
<label index="31" x="48" y="97" z="60">Sagittal stratum (include inferior longitidinal fasciculus and inferior fronto-occipital fasciculus) R</label>
<label index="32" x="131" y="97" z="60">Sagittal stratum (include inferior longitidinal fasciculus and inferior fronto-occipital fasciculus) L</label>
<label index="33" x="58" y="131" z="64">External capsule R</label>
<label index="34" x="121" y="131" z="64">External capsule L</label>
<label index="35" x="83" y="132" z="105">Cingulum (cingulate gyrus) R</label>
<label index="36" x="97" y="110" z="108">Cingulum (cingulate gyrus) L</label>
<label index="37" x="66" y="101" z="53">Cingulum (hippocampus) R</label>
<label index="38" x="112" y="99" z="54">Cingulum (hippocampus) L</label>
<label index="39" x="62" y="100" z="66">Fornix (cres) / Stria terminalis (can not be resolved with current resolution) R</label>
<label index="40" x="117" y="100" z="66">Fornix (cres) / Stria terminalis (can not be resolved with current resolution) L</label>
<label index="41" x="53" y="103" z="102">Superior longitudinal fasciculus R</label>
<label index="42" x="126" y="103" z="102">Superior longitudinal fasciculus L</label>
<label index="43" x="69" y="121" z="93">Superior fronto-occipital fasciculus (could be a part of anterior internal capsule) R</label>
<label index="44" x="110" y="121" z="93">Superior fronto-occipital fasciculus (could be a part of anterior internal capsule) L</label>
<label index="45" x="55" y="127" z="54">Uncinate fasciculus R</label>
<label index="46" x="123" y="125" z="58">Uncinate fasciculus L</label>
<label index="47" x="60" y="78" z="86">Tapetum R</label>
<label index="48" x="117" y="76" z="87">Tapetum L</label>
  </data>
</atlas>
chrisgorgo commented 8 years ago

Yes - this is it!

On Wed, Jan 6, 2016 at 9:09 AM, Jon Pipitone notifications@github.com wrote:

It's quite simple: specification here http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases-Reference. For example:

<?xml version="1.0" encoding="ISO-8859-1"?>

JHU ICBM-DTI-81 White-Matter Labels Label /JHU/JHU-ICBM-labels-1mm /JHU/JHU-ICBM-labels-1mm /JHU/JHU-ICBM-labels-2mm /JHU/JHU-ICBM-labels-2mm

— Reply to this email directly or view it on GitHub https://github.com/CobraLab/atlases/issues/3#issuecomment-169391777.