Add nifti versions of the atlases and FSL compatible XML

[chrisgorgo]

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]

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]

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]

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:

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 Unclassified Middle cerebellar peduncle Pontine crossing tract (a part of MCP) Genu of corpus callosum Body of corpus callosum Splenium of corpus callosum Fornix (column and body of fornix) Corticospinal tract R Corticospinal tract L Medial lemniscus R Medial lemniscus L Inferior cerebellar peduncle R Inferior cerebellar peduncle L Superior cerebellar peduncle R Superior cerebellar peduncle L Cerebral peduncle R Cerebral peduncle L Anterior limb of internal capsule R Anterior limb of internal capsule L Posterior limb of internal capsule R Posterior limb of internal capsule L Retrolenticular part of internal capsule R Retrolenticular part of internal capsule L Anterior corona radiata R Anterior corona radiata L Superior corona radiata R Superior corona radiata L Posterior corona radiata R Posterior corona radiata L Posterior thalamic radiation (include optic radiation) R Posterior thalamic radiation (include optic radiation) L Sagittal stratum (include inferior longitidinal fasciculus and inferior fronto-occipital fasciculus) R Sagittal stratum (include inferior longitidinal fasciculus and inferior fronto-occipital fasciculus) L External capsule R External capsule L Cingulum (cingulate gyrus) R Cingulum (cingulate gyrus) L Cingulum (hippocampus) R Cingulum (hippocampus) L Fornix (cres) / Stria terminalis (can not be resolved with current resolution) R Fornix (cres) / Stria terminalis (can not be resolved with current resolution) L Superior longitudinal fasciculus R Superior longitudinal fasciculus L Superior fronto-occipital fasciculus (could be a part of anterior internal capsule) R Superior fronto-occipital fasciculus (could be a part of anterior internal capsule) L Uncinate fasciculus R Uncinate fasciculus L Tapetum R Tapetum L

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