Missing info from HOSPA atlas

[wiheto]

So I have noticed 3 issues regarding the HOSPA in the _dseg.tsv file.

1. The dseg.tsv file is missing from: MNI152NLin2009cAsym

2. The brainstem is missing in the _dseg file in MNI152NLin6Asym link. It currently reads:

6   Left Pallidum   54, 62, 35
8   Left Hippocampus    59, 54, 27

The brainstem is included in the nifti image.

3. Finally the index of the dseg starts at zero, but here (and in most atlases) the indexing starts at 1 in the image files. This could lead to greater confusion (for example the brainstem has a value 8 in the nifti file). While the xyz coordinates could be used to find the actual value, perhaps an additional column in the data for this information should be added? (Suggested column name: value)

I can PR a fix for all three of these things unless any of these are meant to be the case.

[wiheto]

Closing as I realized this should be in the templateflow main repo not the template! Will repost there.

[oesteban]

Not sure, those tsv files are here, right?

[wiheto]

They are missing from https://github.com/templateflow/tpl-MNI152NLin2009cAsym (but the atlas is available there). Thats why I opened up an issue on the main template repo to avoid this confusion.

[oesteban]

I think this is the right place for this issue. Let's keep on here.

@wiheto, may I expect a PR from you for the HOSPA labels? I will try to focus on HOCPAL and HOSPA

[wiheto]

Sorry completely forgot about this. Fixed this a while ago for my own use.

may I expect a PR from you for the HOSPA labels? I will try to focus on HOCPAL and HOSPA

I don't understand this comment though. Do you want me to submit a PR or are you focusing on it? Once I've got the answer, I'll submit the PR

[Shotgunosine]

@oesteban or @wiheto Do you know where the full look up table for the HOCPAL atlases is? FSL doesn't have a bilateral HOCPAL atlas. Though looking at what's missing, it's all of the regions from the FSL LUT that have a coma or apostrophe in the name. So perhaps a parsing error somewhere.

<?xml version="1.0" encoding="ISO-8859-1"?>
<atlas version="1.0">
  <header>
    <name>Harvard-Oxford Cortical Structural Atlas</name>
    <shortname>HOCPA</shortname>
    <type>Probabilistic</type>
    <images>
      <imagefile>/HarvardOxford/HarvardOxford-cort-prob-2mm</imagefile>
      <summaryimagefile>/HarvardOxford/HarvardOxford-cort-maxprob-thr25-2mm</summaryimagefile>
    </images>
    <images>
      <imagefile>/HarvardOxford/HarvardOxford-cort-prob-1mm</imagefile>
      <summaryimagefile>/HarvardOxford/HarvardOxford-cort-maxprob-thr25-1mm</summaryimagefile>
    </images>
  </header>
  <data>
<label index="0" x="48" y="94" z="35">Frontal Pole</label>
<label index="1" x="25" y="70" z="32">Insular Cortex</label>
<label index="2" x="33" y="73" z="63">Superior Frontal Gyrus</label>
<label index="3" x="25" y="72" z="55">Middle Frontal Gyrus</label>
<label index="4" x="20" y="77" z="40">Inferior Frontal Gyrus, pars triangularis</label>
<label index="5" x="20" y="71" z="47">Inferior Frontal Gyrus, pars opercularis</label>
<label index="6" x="44" y="51" z="68">Precentral Gyrus</label>
<label index="7" x="61" y="69" z="17">Temporal Pole</label>
<label index="8" x="73" y="59" z="32">Superior Temporal Gyrus, anterior division</label>
<label index="9" x="75" y="52" z="35">Superior Temporal Gyrus, posterior division</label>
<label index="10" x="74" y="59" z="26">Middle Temporal Gyrus, anterior division</label>
<label index="11" x="14" y="51" z="30">Middle Temporal Gyrus, posterior division</label>
<label index="12" x="72" y="35" z="38">Middle Temporal Gyrus, temporooccipital part</label>
<label index="13" x="22" y="61" z="16">Inferior Temporal Gyrus, anterior division</label>
<label index="14" x="70" y="42" z="26">Inferior Temporal Gyrus, posterior division</label>
<label index="15" x="70" y="35" z="29">Inferior Temporal Gyrus, temporooccipital part</label>
<label index="16" x="52" y="42" z="69">Postcentral Gyrus</label>
<label index="17" x="28" y="39" z="63">Superior Parietal Lobule</label>
<label index="18" x="73" y="48" z="53">Supramarginal Gyrus, anterior division</label>
<label index="19" x="72" y="39" z="51">Supramarginal Gyrus, posterior division</label>
<label index="20" x="21" y="37" z="55">Angular Gyrus</label>
<label index="21" x="60" y="28" z="57">Lateral Occipital Cortex, superior division</label>
<label index="22" x="68" y="28" z="38">Lateral Occipital Cortex, inferior division</label>
<label index="23" x="47" y="23" z="40">Intracalcarine Cortex</label>
<label index="24" x="45" y="84" z="27">Frontal Medial Cortex</label>
<label index="25" x="45" y="63" z="63">Juxtapositional Lobule Cortex (formerly Supplementary Motor Cortex)</label>
<label index="26" x="46" y="74" z="27">Subcallosal Cortex</label>
<label index="27" x="45" y="80" z="52">Paracingulate Gyrus</label>
<label index="28" x="45" y="61" z="57">Cingulate Gyrus, anterior division</label>
<label index="29" x="44" y="42" z="54">Cingulate Gyrus, posterior division</label>
<label index="30" x="45" y="31" z="55">Precuneous Cortex</label>
<label index="31" x="45" y="23" z="49">Cuneal Cortex</label>
<label index="32" x="25" y="77" z="29">Frontal Orbital Cortex</label>
<label index="33" x="57" y="62" z="18">Parahippocampal Gyrus, anterior division</label>
<label index="34" x="58" y="45" z="28">Parahippocampal Gyrus, posterior division</label>
<label index="35" x="41" y="22" z="33">Lingual Gyrus</label>
<label index="36" x="62" y="61" z="15">Temporal Fusiform Cortex, anterior division</label>
<label index="37" x="64" y="47" z="24">Temporal Fusiform Cortex, posterior division</label>
<label index="38" x="62" y="37" z="29">Temporal Occipital Fusiform Cortex</label>
<label index="39" x="33" y="23" z="30">Occipital Fusiform Gyrus</label>
<label index="40" x="66" y="74" z="37">Frontal Operculum Cortex</label>
<label index="41" x="19" y="61" z="40">Central Opercular Cortex</label>
<label index="42" x="17" y="50" z="47">Parietal Operculum Cortex</label>
<label index="43" x="20" y="60" z="36">Planum Polare</label>
<label index="44" x="67" y="52" z="39">Heschl's Gyrus (includes H1 and H2)</label>
<label index="45" x="74" y="53" z="40">Planum Temporale</label>
<label index="46" x="44" y="21" z="42">Supracalcarine Cortex</label>
<label index="47" x="37" y="15" z="34">Occipital Pole</label>
  </data>
</atlas>

[oesteban]

@wiheto Do you want me to submit a PR or are you focusing on it?

Yup, that'd be sweet.

@Shotgunosine yes, a parsing error seems like the culprit - I'll take care of this.

[sunyunseung1]

Dear experts,

Is dseg.tsv file for HOPA, HOPAL, HOSPA atlas in MNI152NLin2009cAsym space available somewhere? I am searching for files containing index, name, and coordinate info.

Thanks, Sun