Merge pull request #93 from khanlab/surfarea

new gyrification as surface area ratio

docs/getting_started/outputs.rst

@@ -90,11 +90,11 @@ Surfaces are provided in different density configurations, and are labelled base
 
 All surfaces of the same density (e.g. `2k`), in both ``space-T1w`` and ``space-unfolded``, share the same mesh topology and have corresponding vertices with each other. The vertex locations for unfolded surfaces are identical for all subjects as well (note that this of course is not the case for the ``space-T1w`` surfaces). 
 
-In addition to the geometry files, surface-based shape metrics are provided in ``.shape.gii`` format. The thickness, curvature and gyrification are computed using the same methods as cortical surfaces, based on the surface geometry files, and are provided in the ``T1w`` space::
+In addition to the geometry files, surface-based shape metrics are provided in ``.shape.gii`` format. The thickness, curvature and surface area are computed using the same methods as cortical surfaces, based on the surface geometry files, and are provided in the ``T1w`` space. The gyrification metric is the ratio of native to unfolded surface area, or equivalently, the scaling or distortion factor when unfolding::
 
     sub-{subject}
      └── surf_T2w
-         └── sub-{subject}_hemi-{L,R}_space-T1w_den-{density}_{thickness,curvature,gyrification}.shape.gii
+         └── sub-{subject}_hemi-{L,R}_space-T1w_den-{density}_{thickness,curvature,surfarea,gyrification}.shape.gii
 
 Finally, these files are packaged together for easy viewing in Connectome Workbench, ``wb_view``, in the following ``.spec`` files, for each hemisphere separately, and combined::
 

hippunfold/resources/unfold_template/tpl-avg_space-unfold_den-2k_surfarea.shape.gii

@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<GIFTI xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd"
+       Version="1"
+       NumberOfDataArrays="1">
+   <MetaData>
+      <MD>
+         <Name><![CDATA[AnatomicalStructurePrimary]]></Name>
+         <Value><![CDATA[Invalid]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[ProgramProvenance]]></Name>
+         <Value><![CDATA[Connectome Workbench
+Type: Command Line Application
+Version: 1.4.1
+Qt Compiled Version: 5.7.1
+Qt Runtime Version: 5.7.1
+Commit: unknown
+Commit Date: unknown
+Compiled with OpenMP: YES
+Compiler: c++ (/usr/bin)
+Compiler Version: 6.3.0
+Compiled Debug: NO
+Operating System: Linux
+]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[Provenance]]></Name>
+         <Value><![CDATA[/usr/bin/wb_command -surface-vertex-areas tpl-avg_space-unfold_den-2k_midthickness.surf.gii tpl-avg_space-unfold_den-2k_midthickness.surf.gii.surfarea.shape.gii]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[WorkingDirectory]]></Name>
+         <Value><![CDATA[/scratch/akhanf/1_dev/hippunfold_v0.5.4/hippunfold/resources/unfold_template]]></Value>
+      </MD>
+   </MetaData>
+   <LabelTable>
+      <Label Key="0" Red="1" Green="1" Blue="1" Alpha="0"><![CDATA[???]]></Label>
+   </LabelTable>
+<DataArray Intent="NIFTI_INTENT_NORMAL"
+           DataType="NIFTI_TYPE_FLOAT32"
+           ArrayIndexingOrder="RowMajorOrder"
+           Dimensionality="1"
+           Dim0="2004"
+           Encoding="GZipBase64Binary"
+           Endian="LittleEndian"
+           ExternalFileName=""
+           ExternalFileOffset="0">
+   <MetaData>
+      <MD>
+         <Name><![CDATA[Name]]></Name>
+         <Value><![CDATA[vertex areas]]></Value>
+      </MD>
+   </MetaData>
+   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d+bEG7xy78C/6AdC7mmhLPncFu4VIMYd3VRSi1FaZj3LVKfWeIXhUCnSfT0TrfB2pcjnn3TOhE6yNh/GmU1J5FnL09QueXcfP4DegYOKA4oBCnVNMhn+6Pb4+CsW5kJFS5Wn35rhBxOofDdvYw5+yO/QbYMqEadpy9TyMOe0ckwZdbF779Itb1nMLJb7egULsUD/4zhyPnn/9jHwZcvLD3G8PL5lCo6Z/hchgmO7zC5LOVUOVyb0cloZKr9/KmJxLyzXFc/xD4n/rhw1d37HmXA/tqP+RvPoWOtESAy69/dBaLhHNxb95SPJzpBy8uP2hhHF6eTELvnv343JmHhqlJyLnFg39OACyfOyOw2h2v5BPxlpsJHnZsw82rMxGUPhqHLHnYoTsFhkffMK93N9hg3UNYL72F5VOvgH/RB/in+8JZKxEN7nqQVA3AreYwRFmGIGDVegQ+8EPRs+kYkNDGFw6Hvh6CslY0Nr9WgPrzXGzg2LP/PCSdImHheh8KVRfx/JQFNLo+4rfBFcSePwe5o6rYvtSfmz3VIdSWiS162kg8mwm1aaex22cJljdbDWtwMOL2/WQu5jLZHVlG/nh33xuZXI2xs9WH2X6nMXTvJcJwjCX+SuXjwJccPFLcgSf2x3FydDFuzjyJWeoJKDguDn2unnLCObx6bwfZKw7gy7/D7eNGEM/fCx2ls7jOrWtquoIJa/cjfXYhHgp5oLD4CUqVdmChpwkyDBbhDldj7uUKbBK2wk1Ol3J7S1dAGG5y0Hubxa1Thx73G68FjSFgkDZcR4vLy+FqD9Ufsm24eoE9GejL0EUtFxvqdyznH+Ihu46LD13b/bUmeBHtg5tczf+PD/mHbIHU53idFg8hloPxbn5YdCRi+PqGcurjInChjjsvbNMbvt+i25QR7WowfN+L124b7oeXcR0bfy5F3cN4PNePhyTXc1uqDiq4mkPPJdDuPELzg1HG9TIUG/JFcrWmV61C95u/eKn0vz13+nP7bO8BqF6eikO6QfiyaDcL25iKm2WG9CJ2Kh0UqcQ+dx/s/nAMeUEBaOv0wPv6VJbDdwSS5hvhMmIfpDgeO2YbNwsHoEdiPhYn2iDnXATkOL/B17U4mCUHw4ejYbhSH7LpnvBcqgjhBzaYenQOnpfx47l0CPZJSCMhg4fT6zZCZVYwMpV2IyboBDo+BaJl6Tl4eqehZ6AEB3r9UExhKFkmh2stvnh3Mg0/n/hirP4BDOaegWi3H3rFjLArOgEfrU/BYtJRrJ2kCKO17hxfGtYCRTeQ4ncb6cM+RdRw69w3pmPqkcUQ4Q+FO+f/xfnixRJg8e8COsxcMEbTCp83WUB3djJ8zmegTnUpfroFIerSUYiv3wYBVWFamH0cO5ZfYY5FPMh+XIKXriJ4d/kqdA73sdSuRLw85QUl1xHoXPQGSm5amNOdiXBu1hw/Zg02m+fD8MQcmGnIQEdUCpna6xEzTQv/5STjrsxWbJ+xDsue7oN4zixIj3LiOBkJZquHdcfms3gflIqrX08Nx9VGxMBpejAUuLnqNcmBNs5D0U9d8Gkm4ZCaAcrqk6Bg5opY8QmYWzgDRTlyUG9eAsupxeyAhz8cT2eyCK4vl2dBiOd4N3df2s2S4B8xBVrcmerHuwgoW2vi70RLyFp4wZnT1zg9ZCMsCozr6T+uj92bg4f1EGr4n7JR2tXwTTuDFW9PMJOoLLxcbgGfsbZoGFAF2QRAedFaCNYvQ9fS2YBFPG6bdTIl5xUIEJPCvIMKOBJnjV0Zflg7Sw8iHMb9Hw9B7ps8/srKoMCwEU7d0VCuyWfVEyeiLVAen/4UsKrWBTjpLoumJYsQbSaMsVoGkNX/D5i5EOeLZKDdPRplQRq4EagBcHxFzB6v57ki7sE1xC32RN/0NMSN24nLN4wgxzOBlIcaftrNxO3fCcjZKQ//IndElPmgKfAA5iw7g3BfR7jsXALl5d6geBXwyTvjUMeg7grj5bqOHMfUJMNEbA6MOD3g+U532sIUbOWbTDesdKAbdZXNf/uQ3ZBrg1HjAijedIE6zxfXT8ZB6Ystpig4YvVfU7h2mSBRRw9vuHdtklU4jCL5UftlA95nqeEOL4XtuzkHbn1taKhcggu1dty8FYZ/sXlsde843B4dg/ciduh+PQEL1nH7ipY2sj42sLOtr9iRXdPw96IxdLqfIaROAXX7bLFZoF234Z02JnyNRgfPAlLJm6BxLhlZAesxXcwAa6Zaw6ErHDpn43B/oTW8c33guW4NjA7OAc97KdyvLkC3qhOemodg96sJcDLtZ30Ru1FlOZp0rZKhVGEGnZmLWM5pH+ydG4rcsFXcWfQU3gZtgKj8SXyrlUfwpP/gwqGt9RqceEDdG092znA9rorLwv9ODDNaMQlPqwHZ2XlMrnQitMS18EP6KFamyWOMbyEbZMKwjZeAZbUGQldcQO4mNxhc2QXN7Bus0vwFws2amWa/Ir4Ix+GR/AUWEegE3Z5dkGnegOJycTQbbkH6wV6s2HoaTwRs0K01Ewv+C0G6hgcWLfbBv34hKlLlx1PNM3BJJPQ37cG+VVfZ5oPzkFZjhpaZIvA8PB/VAsJ42WIPd8sMxov3Qvo1YZT8fcPO+CTho5M7vGMKmQ8Hfx8DNiNCAg2mZ9mbv97o/8EHOjEbZSsO4jf3/yeTGMlWCvSwvVM6mCcyUa6bDDdnbk/yXYk9WfuZ0IgV+LjgOUsT0oX8mSKWoX8eRoZ+CNXiR25zCtNcchDWH/Jh5qiNr8cI7WpjEfRhOcYErUShXD4TJyN8uxbBuq9zZ2fHReC5vmP7tvxkVhd3swXbPKFXVMseujeztjXjYJ51h3nMLWZHpiRBdPJ0TJjpgmaRxRhzZRG0DUSQYX4DpyIvsbby52yC6zb8PDURt14I4LfqISwKT2NTXj1nv+5OwYZnE7DsAT9OOC7B4sYvTDhVHAZHtRCrksEcNNcg8tBWmC09zZzSDaGxKYS9xWrE7NFAu5sv253awrZ8HofRPzPZpKrxWHLcEYlr1RCKtbCf8Yl5/BkDJyUF7P3Ah7K247A4MhZ1ld2sWzeN6WubgvdMFP3JVWyTTSQ7xG8Kt8pBdidOAhnTpNFl8B+bUmzNpAvVmaitKZZ6X2bRI94wbWkhZlw6GgtKHzLZhCx2O2kMxronMweeHMa4LoZcfySrGWOLNy8Nwa/qyxQ41JZmMRxLZ9tECti8Xc/ZytYgJimfx/SyiplJfhGrn5vKjKadYcGTxiI7bAZOmvmy8N0TMavxFvNpOshe/wlkXW8z2dPomezA9nRms8WXtVy7yJyj25jf6nI2+DaWXZHNY/vjr7KYDQms2tyL5Zf90e3RlcD6pq/sRHUHC8yQQQJ/F0vYcIhV773Hahc4sZKmOOYTHsiE3OKYeVk8+7IzhqlbhDL2xYVB3IWljvnMJA9743FtPDO6m4LGP0KYUW+AgUxx7G0LZ7I1EazctJvlWrox+8TzbHJnHCs/GMkkJePYff0aZs72oOpwN0b1vmAhcc/ZnvHVrFw+i+XnrmQNCX6sxHwNKDWbdXx+i7YVQnAWTGJZstMR+uInO5Z/mQWqvmFrgnWY9g8xuK59z569D2Bmh9t0nT8sxjepCahzCGPyBV/ZGmtHZledyFxyl7Alftas7JUJnLcrQnl2EnuXw73fYS+Ynsc7dnn/eDbp3TE25cQNduveeXY7zhSKUX74uF0EPdrluv1SCnBYo8CW+E+GUu4+tGlWMM9Nf9lP/bE4LDnI/MQPsw3JYaxG/QhzmH+KGe+QRoarMTuxr4vtm7AcYjKRbHlwI/NYtgsT+4IZJhyF14a9LMb8CPvO3NmkgnnQChBBas5YiL8UhV1sIKYoPmRr1YIwct0q7hnwkPwhiKVMiGSK466y1yburEktnvUIdDINuzw2J3QqfHijINhczTbm5CFWX47l/znAmkftZJkh3SxKQQaj1CxYR99Ylj7yDrOzT9Ot/rkK4r6zIBkniBoTPri01TH1ETxUO6WzLf2OTH2KDRPy28GmCe1kf0fvZC555sxm+17mI+3Lrtff0+28WMmiDF+xpWb67I4THxqXCWP8gD2r77Bl4p9tWbHcTibjZst60yYNr5+t4s5S9/9hoq8vsbunXNiSyk52Y3EsE377ir0UHGTv311iDQoGDIEOrEBbg/VydfQCN7PTyofgWuKN8iwfVvxzNrMU+MzavKRRqhLHBPR1MaLSgjWbieI8P4+JPulkDjusmLF/CvOb3M+cYvLZtko5KBePRPihNNb7pIolfRrJnZH4UcausrySWHZ1bwY7XTvISsWJiZa8ZoEdqux/ALFpcI0=</Data>
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