Re: [HCP-Users] Visualizing Greyordinate Masks
Oh okay, I see it now. Thank you very much! - Cathy Am Mi., 10. Okt. 2018 um 21:49 Uhr schrieb Timothy Coalson : > The surfaces are fine, we generally recommend very_inflated for viewing > data. To expand on what Matt said, the data in the map you are displaying > in that image appears to have an unusual distribution, with most values > near the minimum value, and a few spots with higher values (or perhaps the > palette coloring in the file doesn't match that map well). Clicking the > wrench icon on the layer will show you a histogram of the values in that > map, and let you change the settings for how the values get colored. You > may also want to look at a volume view to see if anything shows up in the > subcortical structures or cerebellum. > > Tim > > > On Wed, Oct 10, 2018 at 2:20 PM, Glasser, Matthew > wrote: > >> Try changing the color windowing. >> >> Matt. >> >> From: Cathy Chen >> Date: Wednesday, October 10, 2018 at 7:55 AM >> To: Matt Glasser >> Cc: "hcp-users@humanconnectome.org" >> Subject: Re: [HCP-Users] Visualizing Greyordinate Masks >> >> Hi Matt, >> >> I loaded the file as an overlay with the various .surf.gii files in the >> folder >> "100206_3T_Structural_preproc\100206\MNINonLinear\fsaverage_LR32k". When >> I step through the 15 images corresponding to the 15 parcellation >> dimensions, I see very sparse visualizations. For example, this is the >> visualization I got corresponding to one of the parcellation dimensions: >> [image: image.png] >> I'm not sure if I'm using the wrong surface files, or if I need to >> re-save the .dtseries.nii file (to have 1s and 0s rather than the >> regression coeffecients), or if there is something else I need to change or >> add. >> >> Best, >> Cathy >> >> Am Mi., 10. Okt. 2018 um 04:14 Uhr schrieb Glasser, Matthew < >> glass...@wustl.edu>: >> >>> Steve and I think you have the right file, but are not understanding >>> what is confusing about viewing that file in Connectome Workbench, assuming >>> you have loaded the appropriate surfaces and volumes. >>> >>> Matt. >>> >>> From: on behalf of Cathy Chen < >>> c...@alumni.princeton.edu> >>> Date: Tuesday, October 9, 2018 at 9:11 AM >>> To: "hcp-users@humanconnectome.org" >>> Subject: [HCP-Users] Visualizing Greyordinate Masks >>> >>> Dear HCP experts, >>> >>> I'm working with subject-specific parcellations (for instance, " >>> HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_Z\100206.dtseries.nii" >>> ) and would like to visualize the greyordinates corresponding to each of >>> the 15 (or 25, 50, or 100) spatial maps. >>> >>> I've been using Connectome Workbench, but have not been able to figure >>> out a way to do this based on online tutorials -- is it possible to >>> visualize these maps with Connectome Workbench? Would I need to save new >>> versions of the data, so that the maps lie in a [num_grayordinates x >>> num_maps] matrix rather than a [num_maps x num_grayordinates] matrix? >>> >>> Best, >>> Cathy >>> >>> ___ >>> HCP-Users mailing list >>> 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 >> > > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Visualizing Greyordinate Masks
Hi Matt, I loaded the file as an overlay with the various .surf.gii files in the folder "100206_3T_Structural_preproc\100206\MNINonLinear\fsaverage_LR32k". When I step through the 15 images corresponding to the 15 parcellation dimensions, I see very sparse visualizations. For example, this is the visualization I got corresponding to one of the parcellation dimensions: [image: image.png] I'm not sure if I'm using the wrong surface files, or if I need to re-save the .dtseries.nii file (to have 1s and 0s rather than the regression coeffecients), or if there is something else I need to change or add. Best, Cathy Am Mi., 10. Okt. 2018 um 04:14 Uhr schrieb Glasser, Matthew < glass...@wustl.edu>: > Steve and I think you have the right file, but are not understanding what > is confusing about viewing that file in Connectome Workbench, assuming you > have loaded the appropriate surfaces and volumes. > > Matt. > > From: on behalf of Cathy Chen < > c...@alumni.princeton.edu> > Date: Tuesday, October 9, 2018 at 9:11 AM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] Visualizing Greyordinate Masks > > Dear HCP experts, > > I'm working with subject-specific parcellations (for instance, " > HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_Z\100206.dtseries.nii" > ) and would like to visualize the greyordinates corresponding to each of > the 15 (or 25, 50, or 100) spatial maps. > > I've been using Connectome Workbench, but have not been able to figure out > a way to do this based on online tutorials -- is it possible to visualize > these maps with Connectome Workbench? Would I need to save new versions of > the data, so that the maps lie in a [num_grayordinates x num_maps] matrix > rather than a [num_maps x num_grayordinates] matrix? > > Best, > Cathy > > ___ > HCP-Users mailing list > 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. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Visualizing Greyordinate Masks
Dear HCP experts, I'm working with subject-specific parcellations (for instance, " HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_Z\100206.dtseries.nii" ) and would like to visualize the greyordinates corresponding to each of the 15 (or 25, 50, or 100) spatial maps. I've been using Connectome Workbench, but have not been able to figure out a way to do this based on online tutorials -- is it possible to visualize these maps with Connectome Workbench? Would I need to save new versions of the data, so that the maps lie in a [num_grayordinates x num_maps] matrix rather than a [num_maps x num_grayordinates] matrix? Best, Cathy ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Converting greyordinates to
Hi Tim and Matt, Thanks for the quick replies! I wanted to use a nifti file such as " 3T_tfMRI_MOTOR_preproc\100206\MNINonLinear\Results\tfMRI_MOTOR_LR\tfMRI_MOTOR_LR.nii" (in 91x109x91 space) with a parcellation such as " HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_Z\100206.dtseries.nii" (in 91282 greyordinate space). Also, I noticed files such as " 3T_tfMRI_MOTOR_preproc\100206\MNINonLinear\Results\tfMRI_MOTOR_LR\tfMRI_MOTOR_LR_Atlas.dtseries.nii" and " 3T_tfMRI_MOTOR_preproc\100206\MNINonLinear\Results\tfMRI_MOTOR_LR\tfMRI_MOTOR_LR_Atlas_MSMAll.dtseries.nii" -- are these the tfMRI timeseries data already converted to 91282 greyordinate space (ie could I use these files in lieu of trying to convert the tfMRI_MOTOR_LR.nii files from 91x109x91 space to greyordinate space)? Best, Cathy Am Di., 2. Okt. 2018 um 22:47 Uhr schrieb Timothy Coalson : > If you mean the fact that the HCP MMP v1.0 doesn't include any subcortical > indices, you can use "wb_command -cifti-create-dense-from-template" to > expand it to the standard 91282 grayordinates. However, the > -cifti-parcellate command will allow you to use it on standard 91282 > grayordinate data as-is. > > Tim > > > On Mon, Oct 1, 2018 at 3:15 PM, Cathy Chen > wrote: > >> Hello, >> >> I hope you're doing well. >> >> Is there a way to convert greyordinates (such as the system used in >> subject-specific parcellations in the July 2017 release) to the system used >> in other nifti files in the HCP datasets (such as the processed tfMRI data >> in the 1200 subjects release)? I would like to use these two datasets >> together, but have had trouble mapping them to each other. >> >> Sorry if I missed this in the documentation or elsewhere! >> >> Best, >> Cathy >> >> ___ >> HCP-Users mailing list >> 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
[HCP-Users] Converting greyordinates to
Hello, I hope you're doing well. Is there a way to convert greyordinates (such as the system used in subject-specific parcellations in the July 2017 release) to the system used in other nifti files in the HCP datasets (such as the processed tfMRI data in the 1200 subjects release)? I would like to use these two datasets together, but have had trouble mapping them to each other. Sorry if I missed this in the documentation or elsewhere! Best, Cathy ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
