That isn’t the deformed sphere. The spheres are in the Native folder and are
GIFTI files. They will have names like
${Subject}.${Hemisphere}.sphere.MSMAll.surf.gii. The template spheres will be
in the 164k folder and have no MSMAll in them. I would also recommend using
the MSMAll midthickness surfaces for the resampling so that the vertex areas
are appropriately handled. Give a shot at constructing the command line and
I’ll correct it if its wrong.
Peace,
Matt.
From: "Ho, Wilson Christopher"
<w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>>
Date: Monday, January 22, 2018 at 1:51 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll data in HCP_1200 set
Hi Matt,
Thank you for that explanation, it looks like 168038 and a few others are
indeed missing the fMRI data, which would explain the missing files.
For the latter question (generating 164k Myelin Maps with MSMAll without BC), I
found a post
(https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03480.html)
where you advised using wb_command’s -cifti-resample. To clarify, the input
CIFTI should be MyelinMap.164k_fs_LR.dscalar.nii, so should the template used
be the SphericalDistortion_MSMAll.164k_fs_LR.dscalar.nii (aka the deformed
sphere?)
Thanks again,
Wilson
From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Date: Monday, January 22, 2018 at 2:19 PM
To: "Ho, Wilson Christopher"
<w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll data in HCP_1200 set
Are you using a group of subjects that had fMRI data? They are required for
MSMAll. There should be 164k and 32k versions of the MSMAll aligned myelin
maps.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ho, Wilson Christopher"
<w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>>
Date: Monday, January 22, 2018 at 1:16 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll data in HCP_1200 set
Hello HCP experts,
I have a question about the MSMAll data. I know it’s advised to use the MSMAll
variants of maps and surfaces for group analyses but some subjects are missing
these (from what I’ve attempted to pull from the Amazon S3 database ). Take for
example subject 168038, which has:
* 168038.MyelinMap_BC.164k_fs_LR.dscalar.nii
* 168038.MyelinMap.164k_fs_LR.dscalar.nii
Missing however is a 168038.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii that a
lot of other subjects have; this is the case with both 164k and 32k resolutions.
Next, does the 164k-resolution preclude MSMAll-only data? Many subjects have:
* MyelinMap.164k_fs_LR.dscalar.nii
* MyelinMap_BC.164k_fs_LR.dscalar.nii
* MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii
At the 32k resolution I notice they have the aforementioned, as well as a
MyelinMap_MSMAll.32k_fs_LR.dscalar.nii (non-BC, MSM-only).
In these situations would it be advisable to run the analysis on what is
available (eg. non-BC, non-MSMAll), or to reprocess these data (perhaps using
the unprocessed versions) to obtain the missing files? Also, do we know if the
data are yet to be added, or were they excluded due to other factors?
Thank you!
--
Wilson Ho
Programmer/Clinical Research Coordinator
MGH Center for Addiction Medicine
101 Merrimac St. Suite 320
Boston, MA 02114
Tel: 617-724-0367
w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
