Hi Nicola, Can you have a look at where that ROI falls on this file:
https://github.com/Washington-University/Pipelines/blob/master/global/templates/standard_mesh_atlases/Avgwmparc.nii.gz Thanks, Matt. From: Nicola Toschi <[email protected]<mailto:[email protected]>> Date: Sunday, November 27, 2016 at 11:18 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, hcp-users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Regions "missing" in grayordinate space? Hi Matt, thanks for your quick reply. What I meant is that, when looking outside of the cortex, greyordinate space does not appear to cover the whole _rest of_ the brain. Attached, in green what (I believe) is the full subcortical part represented in greyordinate space, and in red (as an example) a ROI we are interested in studying which does not appear to have a "place" in greyordinate format. Please let me know if I am explaining this in a comprehensible way! Thanks in advance Nicola On 11/26/2016 5:41 PM, Glasser, Matthew wrote: Hi Nicola, Can you post an image showing what you think is missing? The amygdala voxels are defined by the “mode” volume parcellation of FreeSurfer on the Conte 69 individual datasets. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Nicola Toschi <[email protected]<mailto:[email protected]>> Date: Thursday, November 24, 2016 at 3:52 AM To: Stephen Smith <[email protected]<mailto:[email protected]>>, Jennifer Elam <[email protected]<mailto:[email protected]>> Cc: hcp-users <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Regions "missing" in grayordinate space? Dear List, a basic question about greyordinate space. Am I right is saying that these are technically not whole brain when looking at subcortical structures? We have been looking at volumetric (subcortical) maps resulting from computing-seed based connectivity starting from MIGP dense PCASeries (wb_command -cifti-average-roi-correlation.), and have noticed that the resulting correlation maps are not "fully" dense in the subcortical regions (e.g. around the amygdala). Thanks in advance! Nicola On 7/14/2016 3:25 PM, Stephen Smith wrote: Hi [comment also for Jenn below] Sorry, we didn't calculate z-stat versions of the volumetric group-average maps. The volumetric maps are really just intended as a useful visual reference - the CIFTI versions are the "real thing". --------------------------------- BTW - I think that you are not asking about subject-specific RSN maps - but for completeness: just the CIFTI z-stat versions of those are available online at HCP website. Jenn - I've just noticed that the descriptions of these 3 recent packages are totally wrong - that's probably my fault sorry - please could you change all of the following text from: The following links contain volumetric NIFTI versions of the CIFTI MSMall Group-ICA parcellations, with various ICA dimensionalities applied. Volumetric Parcellations for 10-, 25-, 50-, 100-dimensionalities (57GB)<https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=GroupAvg&filePath=HCP_S900_PTNmaps_d15_25_50_100.zip> Volumetric Parcellations for 200-dimensionality (55GB)<https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=GroupAvg&filePath=HCP_S900_PTNmaps_d200.zip> Volumetric Parcellations for 300-dimensionality (85GB)<https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=GroupAvg&filePath=HCP_S900_PTNmaps_d300.zip> to being: The following links contain subject-specific CIFTI maps: subject-specific versions of the group-ICA parcellations, with various ICA dimensionalities applied. These are z-statistic maps generated using dual-regression. CIFTI subject-specific Parcellations for 10-, 25-, 50-, 100-dimensionalities (57GB)<https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=GroupAvg&filePath=HCP_S900_PTNmaps_d15_25_50_100.zip> CIFTI subject-specific Parcellations for 200-dimensionality (55GB)<https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=GroupAvg&filePath=HCP_S900_PTNmaps_d200.zip> CIFTI subject-specific Parcellations for 300-dimensionality (85GB)<https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=GroupAvg&filePath=HCP_S900_PTNmaps_d300.zip> Thanks! On 14 Jul 2016, at 06:49, Nicola Toschi <[email protected]<mailto:[email protected]>> wrote: Dear Prof. Smith, Dear List, one more question: would the Z-maps related to the second-last step step (dual regression to create volumetric representations if the IC) be available (they are not in the public release)? This would greatly aid in interpreting/threshold the volumetric betas. Thanks a lot in advance, Nicola On 07/06/2016 10:09 AM, Stephen Smith wrote: Hi Group-ICA is carried out in grayordinate space. Then: For each subject, subject-wise grayordinate AND volumetric maps (versions of the group-ICA) are estimated using dual-regression, with node-timeseries normalisation, and outputs in units of GLM betas (parameter estimates) not Z. These volumetric maps are then averaged across subjects to generate the group-average volumetric maps distributed from HCP. So how you threshold these is up to you and depends what the intended usage for that is....... Cheers. On 6 Jul 2016, at 07:26, Nicola Toschi <[email protected]<mailto:[email protected]>> wrote: Hi, The volumetric version! Thanks in advance, Nicola -------- Original message -------- From: Stephen Smith <[email protected]<mailto:[email protected]>> Date: 04/07/2016 12:37 PM (GMT+01:00) To: Nicola Toschi <[email protected]<mailto:[email protected]>> Cc: hcp-users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Exact Meaning of ICA maps in 800 subjects release HI - do you mean the grayordinate or volumetric versions? Cheers On 4 Jul 2016, at 11:16, Nicola Toschi <[email protected]<mailto:[email protected]>> wrote: Hi list, This may be more of a MELODIC question, but I would be grateful for any input: In the ICA release on 800+ subjects, what is the exact mathematical meaning / definition of the (non-binary) intensities of the different component volumes? Are they easily relatable to a statistical map (I am looking to threshold them to study main clusters and possibly correct for multiple comparisons)? Thanks in advance, Nicola _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected]<mailto:[email protected]> http://www.fmrib.ox.ac.uk/~steve<http://www.fmrib.ox.ac.uk/%7Esteve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet<http://smithinks.net/> _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users --------------------------------------------------------------------------- Stephen M. 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Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected]<mailto:[email protected]> http://www.fmrib.ox.ac.uk/~steve<http://www.fmrib.ox.ac.uk/%7Esteve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet<http://smithinks.net> ________________________________ [Avast logo]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> This email has been checked for viruses by Avast antivirus software. www.avast.com<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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