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zenodo40/100

Grey-white matter contrast surface files in ABIDE 1&2 datasets

<p>Computed with FreeSurfer.</p> <p>https://surfer.nmr.mgh.harvard.edu/</p> <p>ABIDE dataset:</p> <p>http://fcon_1000.projects.nitrc.org/indi/abide/</p> <p>Used in:</p> <p>Fouquet, M., Traut, N., Beggiato, A., Delorme, R., Bourgeron, T., &amp; Toro, R. (2019). Increased contrast of the grey-white matter boundary in the motor, visual and auditory areas in Autism Spectrum Disorders. <em>BioRxiv</em>, 750117. <a href="https://doi.org/10.1101/750117">https://doi.org/10.1101/750117</a></p> <p>https://github.com/neuroanatomy/GWPC</p>

opencc-by-4.0Sep 2019View details →
zenodo36/100

Brain surfaces computed with FreeSurfer 6 for all ABIDE I subjects

<p># ABIDE I FreeSurfer 6 &#39;surfaces&#39; data</p> <p><br> This archive contains the following ABIDE I FreeSurfer 6 meshes / surfaces:<br> white, orig, sphere</p> <p>Note that the pial surface is part of the ABIDE I pial lgi dataset:</p> <p>&nbsp;&nbsp; https://zenodo.org/record/7132610<br> &nbsp;&nbsp; DOI: 10.5281/zenodo.7132610</p> <p>&nbsp;</p> <p><br> ## Credits</p> <p>This data is derived from the MRI scans of the ABIDE I dataset:</p> <p>* ABIDE I dataset: https://fcon_1000.projects.nitrc.org/indi/abide/</p> <p>Quoting from that website:</p> <p>&nbsp;&nbsp;&nbsp; &quot;The Autism Brain Imaging Data Exchange I (ABIDE I) represents the first<br> &nbsp;&nbsp;&nbsp;&nbsp; ABIDE initiative. Started as a grass roots effort, ABIDE I involved 17<br> &nbsp;&nbsp;&nbsp;&nbsp; international sites, sharing previously collected resting state functional<br> &nbsp;&nbsp;&nbsp;&nbsp; magnetic resonance imaging (R-fMRI), anatomical and phenotypic datasets<br> &nbsp;&nbsp;&nbsp;&nbsp; made available for data sharing with the broader scientific community.<br> &nbsp;&nbsp;&nbsp;&nbsp; This effort yielded 1112 dataset, including 539 from individuals with<br> &nbsp;&nbsp;&nbsp;&nbsp; ASD and 573 from typical controls (ages 7-64 years, median 14.7 years<br> &nbsp;&nbsp;&nbsp;&nbsp; across groups). This aggregate was released in August 2012. Its<br> &nbsp;&nbsp;&nbsp;&nbsp; establishment demonstrated the feasibility of aggregating resting<br> &nbsp;&nbsp;&nbsp;&nbsp; state fMRI and structural MRI data across sites; the rate of these<br> &nbsp;&nbsp;&nbsp;&nbsp; data use and resulting publications (see Manuscripts) have shown its<br> &nbsp;&nbsp;&nbsp;&nbsp; utility for capturing whole brain and regional properties of the brain<br> &nbsp;&nbsp;&nbsp;&nbsp; connectome in Autism Spectrum Disorder (ASD). In accordance with<br> &nbsp;&nbsp;&nbsp;&nbsp; HIPAA guidelines and 1000 Functional Connectomes Project / INDI<br> &nbsp;&nbsp;&nbsp;&nbsp; protocols, all datasets have been anonymized, with no protected<br> &nbsp;&nbsp;&nbsp;&nbsp; health information included.&quot;</p> <p>Citation: Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., ... &amp; Milham, M. P. (2014).<br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. Molecular psychiatry, 19(6), 659-667.</p> <p>## How this data was produced</p> <p>The following steps were used to create the data:</p> <p>* We downloaded all available MRI scans for the ABIDE I subjects (1035 subjects).<br> * We pre-processed all subjects in FreeSurfer version 6 (https://freesurfer.net) by running the full recon-all pipeline for each subject.<br> &nbsp;&nbsp;&nbsp; - We did not run any quality metrics on the scans or exclude any subjects.</p> <p><br> ## Contained files</p> <p>* In order to reduce the size of this dataset, for each subject, we only included the following files:<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.white&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the white surface for the left hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.white&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the white surface for the right hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.orig&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the orig surface for the left hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.orig&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the orig surface for the right hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.sphere&nbsp;&nbsp;&nbsp;&nbsp; : the sphere surface for the left hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.sphere&nbsp;&nbsp;&nbsp;&nbsp; : the sphere surface for the right hemisphere</p> <p>All files are in binary FreeSurfer surf format and represent triangular meshes.<br> All surfaces are full resolution.</p> <p><br> ## What is NOT contained</p> <p>* The ABIDE demographics information (metadata on the subjects, like age, ...) is not included, you can get it from the ABIDE website.<br> * The pial surface is not included, get it from https://zenodo.org/record/7132610 instead.</p> <p>## Author and License</p> <p>Note: For the authors of the original ABIDE I dataset, see the Credits section above.</p> <p>This lgi data was created by:</p> <p>&nbsp;&nbsp;&nbsp; Dr. Tim Sch&auml;fer<br> &nbsp;&nbsp;&nbsp; Postdoc Computational Neuroimaging<br> &nbsp;&nbsp;&nbsp; Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy<br> &nbsp;&nbsp;&nbsp; University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany<br> &nbsp;&nbsp;&nbsp; http://rcmd.org/ts</p> <p>The data is published under the following license:</p> <p>Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode.txt or the file LICENSE for the full legal code.</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/ for an easy explanation of what this license means for you.</p> <p>&nbsp;</p>

opencc-by-4.0Nov 2022View details →
zenodo36/100

Native space mesh descriptors computed with FreeSurfer 6 for all ABIDE I subjects

<p># ABIDE I FreeSurfer 6 &#39;native space descriptors&#39; data</p> <p><br> This archive contains the following ABIDE I FreeSurfer 6 native space mesh descriptors:<br> thickness, area, volume, sulc, curv, jacobian_white.</p> <p><br> ## Credits</p> <p>This data is derived from the MRI scans of the ABIDE I dataset:</p> <p>* ABIDE I dataset: https://fcon_1000.projects.nitrc.org/indi/abide/</p> <p>Quoting from that website:</p> <p>&nbsp;&nbsp;&nbsp; &quot;The Autism Brain Imaging Data Exchange I (ABIDE I) represents the first<br> &nbsp;&nbsp;&nbsp;&nbsp; ABIDE initiative. Started as a grass roots effort, ABIDE I involved 17<br> &nbsp;&nbsp;&nbsp;&nbsp; international sites, sharing previously collected resting state functional<br> &nbsp;&nbsp;&nbsp;&nbsp; magnetic resonance imaging (R-fMRI), anatomical and phenotypic datasets<br> &nbsp;&nbsp;&nbsp;&nbsp; made available for data sharing with the broader scientific community.<br> &nbsp;&nbsp;&nbsp;&nbsp; This effort yielded 1112 dataset, including 539 from individuals with<br> &nbsp;&nbsp;&nbsp;&nbsp; ASD and 573 from typical controls (ages 7-64 years, median 14.7 years<br> &nbsp;&nbsp;&nbsp;&nbsp; across groups). This aggregate was released in August 2012. Its<br> &nbsp;&nbsp;&nbsp;&nbsp; establishment demonstrated the feasibility of aggregating resting<br> &nbsp;&nbsp;&nbsp;&nbsp; state fMRI and structural MRI data across sites; the rate of these<br> &nbsp;&nbsp;&nbsp;&nbsp; data use and resulting publications (see Manuscripts) have shown its<br> &nbsp;&nbsp;&nbsp;&nbsp; utility for capturing whole brain and regional properties of the brain<br> &nbsp;&nbsp;&nbsp;&nbsp; connectome in Autism Spectrum Disorder (ASD). In accordance with<br> &nbsp;&nbsp;&nbsp;&nbsp; HIPAA guidelines and 1000 Functional Connectomes Project / INDI<br> &nbsp;&nbsp;&nbsp;&nbsp; protocols, all datasets have been anonymized, with no protected<br> &nbsp;&nbsp;&nbsp;&nbsp; health information included.&quot;</p> <p>Citation: Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., ... &amp; Milham, M. P. (2014).<br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. Molecular psychiatry, 19(6), 659-667.</p> <p>## How this data was produced</p> <p>The following steps were used to create the data:</p> <p>* We downloaded all available MRI scans for the ABIDE I subjects (1035 subjects).<br> * We pre-processed all subjects in FreeSurfer version 6 (https://freesurfer.net) by running the full recon-all pipeline for each subject.<br> &nbsp;&nbsp;&nbsp; - We did not run any quality metrics on the scans or exclude any subjects.</p> <p><br> ## Contained files</p> <p>* In order to reduce the size of this dataset, for each subject, we only included the following files:<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.thickness&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex cortical thickness for the left hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.thickness&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex cortical thickness for the right hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.area&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex area of the white surface for the left hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.area&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex area of the white surface for the right hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.volume&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex cortical volume for the left hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.volume&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex cortical volume for the right hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.sulc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex sulcal depth for the left hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.sulc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex sulcal depth for the right hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.curv&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex mean curvature of the white surface for the left hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.curv&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the per-vertex mean curvature of the white surface for the right hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.jacobian_white : the per-vertex jacobian for the left hemisphere<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.jacobian_white : the per-vertex jacobian for the right hemisphere</p> <p>All files are in binary FreeSurfer curv format.</p> <p><br> ## What is NOT contained</p> <p>* The ABIDE demographics information (metadata on the subjects, like age, ...) is not included, you can get it from the ABIDE website.</p> <p>## Author and License</p> <p>Note: For the authors of the original ABIDE I dataset, see the Credits section above.</p> <p>This lgi data was created by:</p> <p>&nbsp;&nbsp;&nbsp; Dr. Tim Sch&auml;fer<br> &nbsp;&nbsp;&nbsp; Postdoc Computational Neuroimaging<br> &nbsp;&nbsp;&nbsp; Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy<br> &nbsp;&nbsp;&nbsp; University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany<br> &nbsp;&nbsp;&nbsp; http://rcmd.org/ts</p> <p>The data is published under the following license:</p> <p>Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode.txt or the file LICENSE for the full legal code.</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/ for an easy explanation of what this license means for you.</p> <p>&nbsp;</p>

opencc-by-4.0Nov 2022View details →
zenodo36/100

Brain labels computed with FreeSurfer 6 for all ABIDE I subjects

<p># ABIDE I FreeSurfer 6 &#39;label&#39; data</p> <p><br> This archive contains the following ABIDE I FreeSurfer 6 labels:<br> cortex, aparc, aparc.a2009s.</p> <p><br> ## Credits</p> <p>This data is derived from the MRI scans of the ABIDE I dataset:</p> <p>* ABIDE I dataset: https://fcon_1000.projects.nitrc.org/indi/abide/</p> <p>Quoting from that website:</p> <p>&nbsp;&nbsp;&nbsp; &quot;The Autism Brain Imaging Data Exchange I (ABIDE I) represents the first<br> &nbsp;&nbsp;&nbsp;&nbsp; ABIDE initiative. Started as a grass roots effort, ABIDE I involved 17<br> &nbsp;&nbsp;&nbsp;&nbsp; international sites, sharing previously collected resting state functional<br> &nbsp;&nbsp;&nbsp;&nbsp; magnetic resonance imaging (R-fMRI), anatomical and phenotypic datasets<br> &nbsp;&nbsp;&nbsp;&nbsp; made available for data sharing with the broader scientific community.<br> &nbsp;&nbsp;&nbsp;&nbsp; This effort yielded 1112 dataset, including 539 from individuals with<br> &nbsp;&nbsp;&nbsp;&nbsp; ASD and 573 from typical controls (ages 7-64 years, median 14.7 years<br> &nbsp;&nbsp;&nbsp;&nbsp; across groups). This aggregate was released in August 2012. Its<br> &nbsp;&nbsp;&nbsp;&nbsp; establishment demonstrated the feasibility of aggregating resting<br> &nbsp;&nbsp;&nbsp;&nbsp; state fMRI and structural MRI data across sites; the rate of these<br> &nbsp;&nbsp;&nbsp;&nbsp; data use and resulting publications (see Manuscripts) have shown its<br> &nbsp;&nbsp;&nbsp;&nbsp; utility for capturing whole brain and regional properties of the brain<br> &nbsp;&nbsp;&nbsp;&nbsp; connectome in Autism Spectrum Disorder (ASD). In accordance with<br> &nbsp;&nbsp;&nbsp;&nbsp; HIPAA guidelines and 1000 Functional Connectomes Project / INDI<br> &nbsp;&nbsp;&nbsp;&nbsp; protocols, all datasets have been anonymized, with no protected<br> &nbsp;&nbsp;&nbsp;&nbsp; health information included.&quot;</p> <p>Citation: Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., ... &amp; Milham, M. P. (2014).<br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. Molecular psychiatry, 19(6), 659-667.</p> <p>## How this data was produced</p> <p>The following steps were used to create the data:</p> <p>* We downloaded all available MRI scans for the ABIDE I subjects (1035 subjects).<br> * We pre-processed all subjects in FreeSurfer version 6 (https://freesurfer.net) by running the full recon-all pipeline for each subject.<br> &nbsp;&nbsp;&nbsp; - We did not run any quality metrics on the scans or exclude any subjects.</p> <p><br> ## Contained files</p> <p>* In order to reduce the size of this dataset, for each subject, we only included the following files:<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/label/lh.cortex.label : label identifying which mesh vertices belong to cortex versus medial wall, for left hemisphere.<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/label/rh.cortex.label : label identifying which mesh vertices belong to cortex versus medial wall, for right hemisphere.<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/label/lh.aparc.annot : Desikan atlas surface parcellation for left hemisphere.<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/label/rh.aparc.annot : Desikan atlas surface parcellation for right hemisphere.<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/label/lh.aparc.a2009s.annot : Destrieux atlas surface parcellation for left hemisphere.<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/label/rh.aparc.a2900s.annot : Destrieux atlas surface parcellation for right hemisphere.</p> <p><br> All files are in ASCII FreeSurfer label format.<br> For the annot files, see FreeSurferColorLut.txt that comes with FreeSurfer for meaning of integers specifying a region.</p> <p>## What is NOT contained</p> <p>* The ABIDE demographics information (metadata on the subjects, like age, ...) is not included, you can get it from the ABIDE website.</p> <p>## Author and License</p> <p>Note: For the authors of the original ABIDE I dataset, see the Credits section above.</p> <p>This label data was created by:</p> <p>&nbsp;&nbsp;&nbsp; Dr. Tim Sch&auml;fer<br> &nbsp;&nbsp;&nbsp; Postdoc Computational Neuroimaging<br> &nbsp;&nbsp;&nbsp; Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy<br> &nbsp;&nbsp;&nbsp; University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany<br> &nbsp;&nbsp;&nbsp; http://rcmd.org/ts</p> <p>The data is published under the following license:</p> <p>Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode.txt or the file LICENSE for the full legal code.</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/ for an easy explanation of what this license means for you.</p> <p>&nbsp;</p>

opencc-by-4.0Nov 2022View details →
zenodo36/100

Brain volumes computed with FreeSurfer 6 for all ABIDE I subjects

<p># ABIDE I FreeSurfer 6 &#39;brain volume&#39; data</p> <p><br> This archive contains the following ABIDE I FreeSurfer 6 volumes:<br> mri/brain.mgz, mri/brain_mask.mgz, mri/aseg.mgz, mri/wm.mgz.</p> <p><br> ## Credits</p> <p>This data is derived from the MRI scans of the ABIDE I dataset:</p> <p>* ABIDE I dataset: https://fcon_1000.projects.nitrc.org/indi/abide/</p> <p>Quoting from that website:</p> <p>&nbsp;&nbsp;&nbsp; &quot;The Autism Brain Imaging Data Exchange I (ABIDE I) represents the first<br> &nbsp;&nbsp;&nbsp;&nbsp; ABIDE initiative. Started as a grass roots effort, ABIDE I involved 17<br> &nbsp;&nbsp;&nbsp;&nbsp; international sites, sharing previously collected resting state functional<br> &nbsp;&nbsp;&nbsp;&nbsp; magnetic resonance imaging (R-fMRI), anatomical and phenotypic datasets<br> &nbsp;&nbsp;&nbsp;&nbsp; made available for data sharing with the broader scientific community.<br> &nbsp;&nbsp;&nbsp;&nbsp; This effort yielded 1112 dataset, including 539 from individuals with<br> &nbsp;&nbsp;&nbsp;&nbsp; ASD and 573 from typical controls (ages 7-64 years, median 14.7 years<br> &nbsp;&nbsp;&nbsp;&nbsp; across groups). This aggregate was released in August 2012. Its<br> &nbsp;&nbsp;&nbsp;&nbsp; establishment demonstrated the feasibility of aggregating resting<br> &nbsp;&nbsp;&nbsp;&nbsp; state fMRI and structural MRI data across sites; the rate of these<br> &nbsp;&nbsp;&nbsp;&nbsp; data use and resulting publications (see Manuscripts) have shown its<br> &nbsp;&nbsp;&nbsp;&nbsp; utility for capturing whole brain and regional properties of the brain<br> &nbsp;&nbsp;&nbsp;&nbsp; connectome in Autism Spectrum Disorder (ASD). In accordance with<br> &nbsp;&nbsp;&nbsp;&nbsp; HIPAA guidelines and 1000 Functional Connectomes Project / INDI<br> &nbsp;&nbsp;&nbsp;&nbsp; protocols, all datasets have been anonymized, with no protected<br> &nbsp;&nbsp;&nbsp;&nbsp; health information included.&quot;</p> <p>Citation: Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., ... &amp; Milham, M. P. (2014).<br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. Molecular psychiatry, 19(6), 659-667.</p> <p>## How this data was produced</p> <p>The following steps were used to create the data:</p> <p>* We downloaded all available MRI scans for the ABIDE I subjects (1035 subjects).<br> * We pre-processed all subjects in FreeSurfer version 6 (https://freesurfer.net) by running the full recon-all pipeline for each subject.<br> &nbsp;&nbsp;&nbsp; - We did not run any quality metrics on the scans or exclude any subjects.</p> <p><br> ## Contained files</p> <p>* In order to reduce the size of this dataset, for each subject, we only included the following files:</p> <p>&nbsp;&nbsp; - &lt;subject&gt;/mri/brain.mgz: the full brain, in FreeSurfer standard orientation (&quot;conformed&quot;)</p> <p>&nbsp;&nbsp;&nbsp; - &lt;subject&gt;/mri/brain_mask.mgz: binary mask separating brain from background</p> <p>&nbsp;&nbsp;&nbsp; - &lt;subject&gt;/mri/aseg.mgz: brain segmentation, assigning voxels to regions. The region code for the voxel values can be found in the FreeSurferColorLUT.txt file that comes with FreeSurfer 6.</p> <p>&nbsp;&nbsp;&nbsp; - &lt;subject&gt;/mri/wm.mgz: binary mask separating white matter from everything else</p> <p>All files are in FreeSurfer MGZ format.</p> <p>## What is NOT contained</p> <p>* The ABIDE demographics information (metadata on the subjects, like age, ...) is not included, you can get it from the ABIDE website.</p> <p>## Author and License</p> <p>Note: For the authors of the original ABIDE I dataset, see the Credits section above.</p> <p>This mri volume data was created by:</p> <p>&nbsp;&nbsp;&nbsp; Dr. Tim Sch&auml;fer<br> &nbsp;&nbsp;&nbsp; Postdoc Computational Neuroimaging<br> &nbsp;&nbsp;&nbsp; Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy<br> &nbsp;&nbsp;&nbsp; University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany<br> &nbsp;&nbsp;&nbsp; http://rcmd.org/ts</p> <p>The data is published under the following license:</p> <p>Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode.txt or the file LICENSE for the full legal code.</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/ for an easy explanation of what this license means for you.</p>

opencc-by-4.0Jun 2023View details →
zenodo36/100

Surface transforms (sphere.reg) computed with FreeSurfer 6 for all ABIDE I subjects

<p># ABIDE I FreeSurfer 6 &#39;surface transforms&#39; data</p> <p><br> This archive contains files needed to map surface-based subject data to other subjects, templates or spaces.</p> <p><br> ## Credits</p> <p>This data is derived from the MRI scans of the ABIDE I dataset:</p> <p>* ABIDE I dataset: https://fcon_1000.projects.nitrc.org/indi/abide/</p> <p>Quoting from that website:</p> <p>&nbsp;&nbsp;&nbsp; &quot;The Autism Brain Imaging Data Exchange I (ABIDE I) represents the first<br> &nbsp;&nbsp;&nbsp;&nbsp; ABIDE initiative. Started as a grass roots effort, ABIDE I involved 17<br> &nbsp;&nbsp;&nbsp;&nbsp; international sites, sharing previously collected resting state functional<br> &nbsp;&nbsp;&nbsp;&nbsp; magnetic resonance imaging (R-fMRI), anatomical and phenotypic datasets<br> &nbsp;&nbsp;&nbsp;&nbsp; made available for data sharing with the broader scientific community.<br> &nbsp;&nbsp;&nbsp;&nbsp; This effort yielded 1112 dataset, including 539 from individuals with<br> &nbsp;&nbsp;&nbsp;&nbsp; ASD and 573 from typical controls (ages 7-64 years, median 14.7 years<br> &nbsp;&nbsp;&nbsp;&nbsp; across groups). This aggregate was released in August 2012. Its<br> &nbsp;&nbsp;&nbsp;&nbsp; establishment demonstrated the feasibility of aggregating resting<br> &nbsp;&nbsp;&nbsp;&nbsp; state fMRI and structural MRI data across sites; the rate of these<br> &nbsp;&nbsp;&nbsp;&nbsp; data use and resulting publications (see Manuscripts) have shown its<br> &nbsp;&nbsp;&nbsp;&nbsp; utility for capturing whole brain and regional properties of the brain<br> &nbsp;&nbsp;&nbsp;&nbsp; connectome in Autism Spectrum Disorder (ASD). In accordance with<br> &nbsp;&nbsp;&nbsp;&nbsp; HIPAA guidelines and 1000 Functional Connectomes Project / INDI<br> &nbsp;&nbsp;&nbsp;&nbsp; protocols, all datasets have been anonymized, with no protected<br> &nbsp;&nbsp;&nbsp;&nbsp; health information included.&quot;</p> <p>Citation: Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., ... &amp; Milham, M. P. (2014).<br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. Molecular psychiatry, 19(6), 659-667.</p> <p>## How this data was produced</p> <p>The following steps were used to create the data:</p> <p>* We downloaded all available MRI scans for the ABIDE I subjects (1035 subjects).<br> * We pre-processed all subjects in FreeSurfer version 6 (https://freesurfer.net) by running the full recon-all pipeline for each subject.<br> &nbsp;&nbsp;&nbsp; - We did not run any quality metrics on the scans or exclude any subjects.</p> <p><br> ## Contained files</p> <p>* In order to reduce the size of this dataset, for each subject, we only included the following files:</p> <p>&nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.sphere.reg: spherical registration information for left hemisphere</p> <p>&nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.sphere.reg: spherical registration information for right hemisphere</p> <p>## What is NOT contained</p> <p>* The ABIDE demographics information (metadata on the subjects, like age, ...) is not included, you can get it from the ABIDE website.</p> <p>## Author and License</p> <p>Note: For the authors of the original ABIDE I dataset, see the Credits section above.</p> <p>This data was created by:</p> <p>&nbsp;&nbsp;&nbsp; Dr. Tim Sch&auml;fer<br> &nbsp;&nbsp;&nbsp; Postdoc Computational Neuroimaging<br> &nbsp;&nbsp;&nbsp; Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy<br> &nbsp;&nbsp;&nbsp; University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany<br> &nbsp;&nbsp;&nbsp; http://rcmd.org/ts</p> <p>The data is published under the following license:</p> <p>Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode.txt or the file LICENSE for the full legal code.</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/ for an easy explanation of what this license means for you.</p>

opencc-by-4.0Jun 2023View details →
zenodo32/100

Local Gyrification Index computed with FreeSurfer 6 for all ABIDE I subjects

<p># ABIDE I FreeSurfer 6 &#39;local gyrification index&#39; (lGI) data</p> <p>DOI of this dataset: 10.5281/zenodo.7132610</p> <p>This directory &#39;abide_freesurfer6_lgi&#39; contains the ABIDE I FreeSurfer 6 &#39;local gyrification index&#39; (lGI) data and meshes.</p> <p><br> ## Credits</p> <p>This data is derived from the MRI scans of the ABIDE I dataset:</p> <p>* ABIDE I dataset: https://fcon_1000.projects.nitrc.org/indi/abide/</p> <p>Quoting from that website:</p> <p>&nbsp;&nbsp;&nbsp; &quot;The Autism Brain Imaging Data Exchange I (ABIDE I) represents the first<br> &nbsp;&nbsp;&nbsp;&nbsp; ABIDE initiative. Started as a grass roots effort, ABIDE I involved 17<br> &nbsp;&nbsp;&nbsp;&nbsp; international sites, sharing previously collected resting state functional<br> &nbsp;&nbsp;&nbsp;&nbsp; magnetic resonance imaging (R-fMRI), anatomical and phenotypic datasets<br> &nbsp;&nbsp;&nbsp;&nbsp; made available for data sharing with the broader scientific community.<br> &nbsp;&nbsp;&nbsp;&nbsp; This effort yielded 1112 dataset, including 539 from individuals with<br> &nbsp;&nbsp;&nbsp;&nbsp; ASD and 573 from typical controls (ages 7-64 years, median 14.7 years<br> &nbsp;&nbsp;&nbsp;&nbsp; across groups). This aggregate was released in August 2012. Its<br> &nbsp;&nbsp;&nbsp;&nbsp; establishment demonstrated the feasibility of aggregating resting<br> &nbsp;&nbsp;&nbsp;&nbsp; state fMRI and structural MRI data across sites; the rate of these<br> &nbsp;&nbsp;&nbsp;&nbsp; data use and resulting publications (see Manuscripts) have shown its<br> &nbsp;&nbsp;&nbsp;&nbsp; utility for capturing whole brain and regional properties of the brain<br> &nbsp;&nbsp;&nbsp;&nbsp; connectome in Autism Spectrum Disorder (ASD). In accordance with<br> &nbsp;&nbsp;&nbsp;&nbsp; HIPAA guidelines and 1000 Functional Connectomes Project / INDI<br> &nbsp;&nbsp;&nbsp;&nbsp; protocols, all datasets have been anonymized, with no protected<br> &nbsp;&nbsp;&nbsp;&nbsp; health information included.&quot;</p> <p>Citation: Di Martino, A., Yan, C. G., Li, Q., Denio, E., Castellanos, F. X., Alaerts, K., ... &amp; Milham, M. P. (2014).<br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. Molecular psychiatry, 19(6), 659-667.</p> <p>## How this data was produced</p> <p>The following steps were used to create the data:</p> <p>* We downloaded all available MRI scans for the ABIDE I subjects (1035 subjects).<br> * We pre-processed all subjects in FreeSurfer version 6 (https://freesurfer.net) by running the full recon-all pipeline for each subject.<br> &nbsp;&nbsp;&nbsp; - We did not run any quality metrics on the scans or exclude any subjects.<br> * We computed pial-lgi (Schaer et al. 2008, https://doi.org/10.1109/TMI.2007.903576) as implemented in FreeSurfer 6 for all subjects.<br> &nbsp;&nbsp;&nbsp; - For some of the subjects, MRI data was not available or lgi could not be computed due to very bad quality of the (or a completely failed) surface reconstruction. These subjects are listed in the file &#39;subjects_lgi_computation_failed.txt&#39; (14 of 1035 subjects).<br> &nbsp;&nbsp;&nbsp; - All subjects for which lgi computation succeeded for both hemispheres are listed in the file &#39;subjects.txt&#39; (1021 of 1035 subjects).</p> <p><br> ## Contained files</p> <p>* In order to reduce the size of this dataset, for each subject, we only included the following files:<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.pial&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the pial surface mesh for the left hemisphere, in FreeSurfer surf format.<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.pial&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : the pial surface mesh for the right hemisphere, in FreeSurfer surf format.<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/lh.pial_lgi&nbsp; : the per-vertex lgi values for the left hemisphere, in FreeSurfer curv format.<br> &nbsp;&nbsp;&nbsp; - &lt;subject&gt;/surf/rh.pial_lgi&nbsp; : the per-vertex lgi values for the right hemisphere, in FreeSurfer curv format.</p> <p>See the section &#39;How this data was produced&#39; for information on the files &#39;subjects.txt&#39; and &#39;subjects_lgi_computation_failed.txt&#39;.</p> <p>## What is NOT contained</p> <p>* The ABIDE demographics information (metadata on the subjects, like age, ...) is not included, you can get it from the ABIDE website.<br> * The lgi values are only contained in native space. Standard space data is available as a separate download on Zenodo.</p> <p>## Author and License</p> <p>Note: For the authors of the original ABIDE I dataset, see the Credits section above.</p> <p>This lgi data was created by:</p> <p>&nbsp;&nbsp;&nbsp; Dr. Tim Sch&auml;fer<br> &nbsp;&nbsp;&nbsp; Postdoc Computational Neuroimaging<br> &nbsp;&nbsp;&nbsp; Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy<br> &nbsp;&nbsp;&nbsp; University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany<br> &nbsp;&nbsp;&nbsp; http://rcmd.org/ts</p> <p>The data is published under the following license:</p> <p>Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode.txt or the file LICENSE for the full legal code.</p> <p>See https://creativecommons.org/licenses/by-nc-sa/3.0/ for an easy explanation of what this license means for you.</p> <p>&nbsp;</p>

openother-ncMar 2022View details →
zenodo28/100

Figure 1 from: Rane S, Jolly E, Park A, Jang H, Craddock C (2017) Developing predictive imaging biomarkers using whole-brain classifiers: Application to the ABIDE I dataset. Research Ideas and Outcomes 3: e12733. https://doi.org/10.3897/rio.3.e12733

Figure 1 - Weights (β-coefficients) for voxel-wise ReHo features from a support vector machine (SVM) classifier mapped on the glass brain to separate individuals with and without Autism Spectrum Disorder

opencc-by-4.0Mar 2017View details →
zenodo28/100

Figure 4 from: Rais M, Ahmed W, Sajjad A, Akram A, Saeed M, Hamid HN, Abid A (2021) Amphibian fauna of Pakistan with notes on future prospects of research and conservation. ZooKeys 1062: 157-175. https://doi.org/10.3897/zookeys.1062.66913

Figure 4 A Karez Frog (Chrysopaa sternosignata) B Ladakh Pelobatid Toad (Scutiger occidentalis) C Ant Frog (Microhyla nilphamariensis) D Marbled Balloon Frog (Uperodon systoma). Photographers: Dr Muhammad Rais (A); Dr Matthias Stöck (B); Chaitanya Shukla (C); Peter Janzen (D).

opencc-by-4.0Oct 2021View details →
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Figure 3 from: Rais M, Ahmed W, Sajjad A, Akram A, Saeed M, Hamid HN, Abid A (2021) Amphibian fauna of Pakistan with notes on future prospects of research and conservation. ZooKeys 1062: 157-175. https://doi.org/10.3897/zookeys.1062.66913

Figure 3 A Skittering Frog (Euphlyctis cyanophlyctis) B Skittering Frog (Euphlyctis kalasgramensis) C Pierrei's Cricket Frog (Minervarya pierrei) D Murree Hills Frog (Nanorana vicina) E, F Burrowing Frog (Sphaerotheca maskeyi). Photographers: Dr Muhammad Rais (A, C–F); Waqas Ali (B).

opencc-by-4.0Oct 2021View details →
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Supplementary material 1 from: Rais M, Ahmed W, Sajjad A, Akram A, Saeed M, Hamid HN, Abid A (2021) Amphibian fauna of Pakistan with notes on future prospects of research and conservation. ZooKeys 1062: 157-175. https://doi.org/10.3897/zookeys.1062.66913

Supplementary tables

opencc-zeroOct 2021View details →
zenodo28/100

Figure 2 from: Rais M, Ahmed W, Sajjad A, Akram A, Saeed M, Hamid HN, Abid A (2021) Amphibian fauna of Pakistan with notes on future prospects of research and conservation. ZooKeys 1062: 157-175. https://doi.org/10.3897/zookeys.1062.66913

Figure 2 A Asian Common Toad or Black-spined Toad (Duttaphrynus melanostictus)B Olive Toad (Duttaphrynus olivaceus) C Indus Valley Toad (Duttaphrynus stomaticus) D Kashmir Torrent Frog (Allopaa barmoachensis) E Hazara Torrent Frog (Allopaa hazarensis) F Indus Valley Bull Frog (Hoplobatrachus tigerinus). Photographers: Dr Muhammad Rais (A, C, E); Dr Spartak Litvinchuk (B); Muhammad Sharif Khan (D); Janis Czurda (F).

opencc-by-4.0Oct 2021View details →
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Figure 1 from: Rais M, Ahmed W, Sajjad A, Akram A, Saeed M, Hamid HN, Abid A (2021) Amphibian fauna of Pakistan with notes on future prospects of research and conservation. ZooKeys 1062: 157-175. https://doi.org/10.3897/zookeys.1062.66913

Figure 1 A Iranian Toad (Bufotes surdus) B Batura Toad (Bufotes baturae) C Himalayan Toad (Duttaphrynus himalayanus) D Ladakh Toad (Bufotes latastii) E Baloch Green Toad (Bufotes zugmayeri) F Swat Green Toad (Bufotes pseudoraddei). Photographers: Dr Spartak Litvinchuk (A–D, F); Muhammad Sharif Khan (E).

opencc-by-4.0Oct 2021View details →
ClinicalTrials.gov24/100

Effects of Activity on Diabetes Risk Among Breast Cancer Survivors on Endocrine Therapy (ABIDE)

ClinicalTrials.gov study NCT06830486. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.

restrictedIPD-UNDECIDEDFeb 2026View details →
ClinicalTrials.gov24/100

Age-Related Macular Degeneration Benchmark Imaging Dataset (ABID)

ClinicalTrials.gov study NCT06924021. IPD Sharing: NO. Countries: 7. Publications: 0.

closedIPD-NOFeb 2026View details →

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