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From: "Glasser, Matthew"
Date: Monday, January 16, 2017 at 10:33 PM
To: "Van Essen, David" , Leah Moreno
, "hcp-users@humanconnectome.org&q
.@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] map data between FreeSurfer and HCP
Dear David and Matt,
Thank you for the specification. Please find attached the rig
.@icloud.com>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] map data between FreeSurfer and HCP
Leah,
I'm not sure exactly what was in your display. But I think what Matt was as
What does it look like if you view the volume surface outline of your
chosen surface on the functional connectivity volume in Connectome
Workbench?
Peace,
Matt.
On 1/16/17, 12:04 AM, "Leah Moreno" wrote:
>Dear Matt,
>
>Thank you very much. Here you have the output of mri_info
>brain.finalsurfs
Dear Matt,
Thank you very much. Here you have the output of mri_info brain.finalsurfs.mgz:
Volume information for brain.finalsurfs.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1., 1., 1.
type: UCHAR (0)
fov: 256.000
dof: 0
Can you post the output of the mri_info command without the grep and such?
Peace,
Matt.
On 1/15/17, 10:11 PM, "Leah Moreno" wrote:
>Dear Matt and experts,
>
>Thank you for your help. Here you have the code from 1 subject and left
>hemisphere:
>
>MatrixX=`mri_info brain.finalsurfs.mgz | grep "c
If you try with the beta version of FreeSurfer the mris_convert command
may take care of what Donna was concerned about automatically or with an
optional flag. That said, I asked you multiple times to provide the exact
commands you were running and any error messages and you have not done
that. I
Thank you, Dona. I tried that too but I am getting similar pictures. Any other
recommendation? I got very nice results from analyses and need nice pictures.
Thanks,
-L
> On Jan 15, 2017, at 10:40 AM, Dierker, Donna wrote:
>
> Hi Leah,
>
> I wonder if you need to apply an affine transform to
Hi Leah,
I wonder if you need to apply an affine transform to your white/pial surfaces
to adjust for the offset between Freesurfer’s origin and your orig.mgz volume’s
origin. See this script:
https://github.com/Washington-University/Pipelines/blob/7cc0bf1863cbc8a1a7ab9c6dd48a25de9be9bae7/PostF
