Hi Matt,
in the file you indicated, it corresponds to the following list of regions
CTX-LH-MEDIALORBITOFRONTAL
LEFT/RIGHT-PUTAMEN
LEFT/RIGHT-VESSEL
WM-LH-INSULA
CTX-LH-UNKNOWN
So to us, it appears that we cannot map this ROI to greyordinate space
because this space it is not fully "dense" subcortically.
Looking forward to your feedback and thanks again.
Nicola
On 11/27/2016 6:22 PM, Glasser, Matthew wrote:
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 <tos...@med.uniroma2.it
<mailto:tos...@med.uniroma2.it>>
Date: Sunday, November 27, 2016 at 11:18 AM
To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>,
hcp-users <hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>>
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: <hcp-users-boun...@humanconnectome.org
<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Nicola
Toschi <tos...@med.uniroma2.it <mailto:tos...@med.uniroma2.it>>
Date: Thursday, November 24, 2016 at 3:52 AM
To: Stephen Smith <st...@fmrib.ox.ac.uk
<mailto:st...@fmrib.ox.ac.uk>>, Jennifer Elam <jse...@gmail.com
<mailto:jse...@gmail.com>>
Cc: hcp-users <hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>>
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 <tos...@med.uniroma2.it
<mailto:tos...@med.uniroma2.it>> 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 <tos...@med.uniroma2.it>
wrote:
Hi,
The volumetric version!
Thanks in advance,
Nicola
-------- Original message --------
From: Stephen Smith <st...@fmrib.ox.ac.uk
<mailto:st...@fmrib.ox.ac.uk>>
Date: 04/07/2016 12:37 PM (GMT+01:00)
To: Nicola Toschi <tos...@med.uniroma2.it
<mailto:tos...@med.uniroma2.it>>
Cc: hcp-users <hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>>
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 <tos...@med.uniroma2.it
<mailto:tos...@med.uniroma2.it>> 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
HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
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)
st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>
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
HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
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)
st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>
http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
Stop the cultural destruction of Tibet <http://smithinks.net/>
---------------------------------------------------------------------------
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)
st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>
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
HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
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. If
you are not the intended recipient, be advised that any unauthorized
use, disclosure, copying or the taking of any action in reliance on
the contents of this information is strictly prohibited. If you have
received this email in error, please immediately notify the sender
via telephone or return mail.
------------------------------------------------------------------------
The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If
you are not the intended recipient, be advised that any unauthorized
use, disclosure, copying or the taking of any action in reliance on
the contents of this information is strictly prohibited. If you have
received this email in error, please immediately notify the sender via
telephone or return mail.
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
