You can use the atlas ROI file:
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii.
Peace,
Matt.
From:
<[email protected]<mailto:[email protected]>>
on behalf of nailin yao <[email protected]<mailto:[email protected]>>
Date: Monday, November 28, 2016 at 3:06 PM
To: Timothy Coalson <[email protected]<mailto:[email protected]>>
Cc: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] group comparison
Thank you Tim! I have now concatenated the myelin maps and going to do the
permutation test with Palm. I plan to do a whole brain vertex level comparison,
do you know which existing mask should I use to group level analysis? Thanks!
Best,
Nailin
2016-11-22 16:48 GMT-05:00 Timothy Coalson
<[email protected]<mailto:[email protected]>>:
wb_shortcuts comes with the latest release of workbench, v1.2.3 - however,
there are a few bugs in the version that was released that way, and a newer
version is available here:
https://github.com/Washington-University/wb_shortcuts
If you want just the script itself, use this link:
https://raw.githubusercontent.com/Washington-University/wb_shortcuts/master/wb_shortcuts
I noticed you used "./wb_command", suggesting that you don't have the workbench
executables in your $PATH. They will need to be in your $PATH in order for
wb_shortcuts to work.
As a final note, there is also wb_command -metric-merge and wb_shortcuts
-metric-concatenate, which do the same thing for .func.gii files, in case you
actually do need to use the non-cifti files.
Tim
On Tue, Nov 22, 2016 at 2:57 PM, nailin yao
<[email protected]<mailto:[email protected]>> wrote:
where can I download wb_shortcuts command? Thanks!
Best,
Nailin
2016-11-22 15:28 GMT-05:00 Harms, Michael
<[email protected]<mailto:[email protected]>>:
Two things:
1) That is not the proper syntax for using -cifti-merge. You need to repeat
the -cifti argument separately for *each* cifti file. I suggest that you use
wb_shortcuts -cifti-concatenate instead to make it simpler.
2) A .func.gii is not a CIFTI file. Use the .dscalar.nii version of the
myelin maps as input.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173<tel:314-747-6173>
St. Louis, MO 63110Email: [email protected]<mailto:[email protected]>
From: nailin yao <[email protected]<mailto:[email protected]>>
Date: Tuesday, November 22, 2016 at 2:14 PM
To: Michael Harms <[email protected]<mailto:[email protected]>>
Cc: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] group comparison
Hi Michael,
I tried the command: ./wb_command -cifti-merge
L.SmoothedMyelinMap.32k_fs_LR.out.func.gii -cifti
*.L.SmoothedMyelinMap.32k_fs_LR.func.gii,
but comes the error:
ERROR: error reading NIfTI file
/gpfs/scratch60/fas/glahn/ny87/Connectivity_Study/myelinmap_analysis/S0009QPW.L.SmoothedMyelinMap.32k_fs_LR.func.gii:
/gpfs/scratch60/fas/glahn/ny87/Connectivity_Study/myelinmap_analysis/S0009QPW.L.SmoothedMyelinMap.32k_fs_LR.func.gii
is not a valid NIfTI file
How can I solve this? Thank you !
Best,
Nailin
2016-11-22 14:14 GMT-05:00 nailin yao
<[email protected]<mailto:[email protected]>>:
Thank you MH!
Best,
Nailin
2016-11-22 13:30 GMT-05:00 Harms, Michael
<[email protected]<mailto:[email protected]>>:
By “compress” do you mean merge into a single file? If so, you can use
wb_command -cifti-merge, or wb_shortcuts -cifti-concatenate. (The latter is a
wrapper that simplifies the merge call). And you can use FSL’s PALM to do a
permutation test.
If 164k is too dense a sampling, there are 32k versions of the myelin maps that
you could use instead.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173<tel:314-747-6173>
St. Louis, MO 63110Email: [email protected]<mailto:[email protected]>
From:
<[email protected]<mailto:[email protected]>>
on behalf of nailin yao <[email protected]<mailto:[email protected]>>
Date: Tuesday, November 22, 2016 at 12:07 PM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] group comparison
Hi,
I want to compare group difference of *L.SmoothedMyelinMap.164k_fs_LR.func.gii
of each subjects. How can I compress the myelinmap of all the subjects and do
the group level permutation test on them? Thank you very much!
Best,
Nailin
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
_______________________________________________
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. 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.
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
________________________________
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.
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
_______________________________________________
HCP-Users mailing list
[email protected]<mailto:[email protected]>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
_______________________________________________
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. 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
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
