Add two gifts files together

Steph

unread,

Jul 23, 2021, 5:42:56 AM7/23/21

to HCP-Users

Dear all,

I have several ....func.gii files and want to add them together in python.

The goal is one overlap func.gii file which combines the other ..func.gii files together

The ..func.gii files are generated from .npy files

1.func.gii+2.func.gii+3....

How to do so?

Steph

unread,

Jul 23, 2021, 5:44:10 AM7/23/21

to HCP-Users, Steph

Sorry, I meant SEVERAL GIFTI files

Glasser, Matthew

unread,

Jul 23, 2021, 7:36:52 AM7/23/21

to hcp-...@humanconnectome.org, Steph

There is wb_command -metric-math.

Matt.

--
You received this message because you are subscribed to the Google Groups "HCP-Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hcp-users+...@humanconnectome.org.
To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/219f2ae8-4090-492c-b4d9-10378a53239bn%40humanconnectome.org.

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.

Coalson, Timothy Scott (S&T-Student)

unread,

Jul 23, 2021, 2:12:32 PM7/23/21

to hcp-...@humanconnectome.org, Steph

Depending on how large "several" is, there is also wb_command -metric-merge and -metric-reduce.

If they are already loaded in python (via nibabel, presumably), you should be able to get the data as a numpy matrix, add those like any other numpy matrix, and put the result into a new gifti file.

Tim

From: Glasser, Matthew <glas...@wustl.edu>
Sent: Friday, July 23, 2021 6:36 AM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Cc: Steph <stephan.wu...@gmail.com>
Subject: Re: [hcp-users] Re: Add two gifts files together

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/78E4A937-3709-4B8E-A2C2-1BBBF3E2754A%40wustl.edu.

Steph

unread,

Oct 5, 2021, 6:34:16 AM10/5/21

to HCP-Users, tsc...@mst.edu, Steph

So I used:

wb_command -metric-resample ses-1_task-rest_Atlas_s0.dtseries_CortexLeft.func.gii L.sphere.32k_fs_LR.surf.gii Sphere.6k.L.surf.gii ADAP_BARY_AREA ses-1_task-rest_Atlas_s0.dtseries_CortexLeft_6k.func.gii -area-metrics sub-1.L.midthickness.32k_fs_LR.surf.gii

but results in

While running:

/Users/neurolab/Desktop/Stephan/Programmes/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -metric-resample ses-1_task-rest_Atlas_s0.dtseries_CortexLeft.func.gii L.sphere.32k_fs_LR.surf.gii Sphere.6k.L.surf.gii ADAP_BARY_AREA ses-1_task-rest_Atlas_s0.dtseries_CortexLeft_6k.func.gii -area-metrics sub-1.L.midthickness.32k_fs_LR.surf.gii

ERROR: NAME OF FILE: sub-1.L.midthickness.32k_fs_LR.surf.gii

All data arrays (columns) in the file must have the same number of rows. The first array (column) contains 32492 rows. Array 2 contains 64980 rows.

Glasser, Matt

unread,

Oct 5, 2021, 9:19:09 AM10/5/21

to hcp-...@humanconnectome.org, tsc...@mst.edu, Steph

Use -area-surfs with a surface.

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/fc3642b2-971d-4361-b156-f47ec99c38een%40humanconnectome.org.

Reply all

Reply to author

Forward