HCPers:
I am trying to understand, in detail, all the HCP pipeline transformations and
what order they are applied to all files. Besides the paper, are there any more
detailed references, diagrams, flowcharts, etc. describing the transformations?
My intent to is be able to interrupt the pipelin
I am trying to simulate the HCP_MEG pipeline (specifically hcp_anatomy) and
thus have to create my own simulated hs_file, as if I had the non-anonymized T1
and a Polhemus headshape file. Can someone tell me how many point are usually
captured in these files?
-Jeff
Hi,
I am calling hcp_anatomy separately to learn how it works so I can adapt it to
EEG. I first tried using megconnectome 3.0 and FieldTrip r10442 as suggested on
the HCP site, but got an error message that a MEX-file was not right. So I
switched to the latest FT version and that problem went a
Schoffelen [mailto:jm.schoffe...@gmail.com]
Sent: Sunday, March 05, 2017 12:58 PM
To: K Jeffrey Eriksen
Subject: Re: [HCP-Users] hcp_anatomy.m needs an hsfile?
The 123456_MEG_headmodel.mat is the volume conduction model: it’s a mesh that
describes the inner surface of the skull.
The hs_file is a binary
, at 21:49, K Jeffrey Eriksen
mailto:eriks...@ohsu.edu>> wrote:
Jan-Mathijs,
Aha, that helps a lot. So I will have to simulate this for my EEG-specific
pipeline. Where can I find the detailed format information so that I may create
my own?
-Jeff
From: Jan Mathijs Schoffelen [mailto:jm.s
ry file that
contains digitized head surface points, which can be used to improve the
coregistration between the anatomical information from the MR-image, and the
MEG sensor-array.
Best,
Jan-Mathijs
On 03 Mar 2017, at 03:00, K Jeffrey Eriksen
mailto:eriks...@ohsu.edu>> wrote:
Sorr
Jan-Mathijs,
I assumed you meant a generic binary file, but is this Mat-file the one?
175237_MEG_anatomy_headmodel.mat
-Jeff
From: Jan Mathijs Schoffelen [mailto:jm.schoffe...@gmail.com]
Sent: Thursday, March 02, 2017 11:13 PM
To: K Jeffrey Eriksen
Cc: Georgios Michalareas (giorgos.michalar
be used to improve the
coregistration between the anatomical information from the MR-image, and the
MEG sensor-array.
Best,
Jan-Mathijs
On 03 Mar 2017, at 03:00, K Jeffrey Eriksen
mailto:eriks...@ohsu.edu>> wrote:
Sorry, meant an HS file.
-Jeff
From:
hcp-users-boun...@humanconnecto
Sorry, meant an HS file.
-Jeff
From: hcp-users-boun...@humanconnectome.org
[mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of K Jeffrey Eriksen
Sent: Thursday, March 02, 2017 5:55 PM
To: Georgios Michalareas (giorgos.michalar...@esi-frankfurt.de)
Cc: hcp-users@humanconnectome.org
Hi again,
Figured out that it really does not need a DICOM file, just a nifti file.
Next problem I ran into was it needs an hcfile. Can anyone tell me exactly what
that is?
-Jeff
From: K Jeffrey Eriksen
Sent: Wednesday, March 01, 2017 4:16 PM
To: Georgios Michalareas (giorgos.michalar...@esi
Georgos,
I got a little further since my last email on this topic. I was able to open a
T1 file after all, and begin marking fiducial points. When it tried to save
them, however, I got this Java error:
Warning: disabling cfg tracking for the time being, due to a Matlab version
related issue
> I
M file from another file such as the 001.mgz file or other volumetric T1?
Thanks,
-Jeff
From: K Jeffrey Eriksen
Sent: Wednesday, March 01, 2017 12:40 PM
To: Georgios Michalareas
Subject: Re: [HCP-Users] MEG_anatomy_transform.txt
Hi Georgos,
I'm back working on this again. I believe what I
substituting the electrode coordinates.
Can you guide me to someone who might be able to advise me on this aspect of
the HCP-MEG pipeline?
Thanks,
-Jeff
From: Michalareas, Giorgos [mailto:giorgos.michalar...@esi-frankfurt.de]
Sent: Tuesday, February 14, 2017 6:00 PM
To: K Jeffrey Eriksen
Cc
y 14, 2017 3:03 PM
To: K Jeffrey Eriksen
Cc: hcp-users@humanconnectome.org
Subject: RE: [HCP-Users] MEG_anatomy_transform.txt
Hi Jeff,
there no need to run the HCP-MEG pipeline on your anatomical file. I am not
sure f you can even do this if you also dont have the MEG head positioning
informatio
] On Behalf Of K Jeffrey Eriksen
Sent: Tuesday, February 14, 2017 3:42 PM
To: Michalareas, Giorgos
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] MEG_anatomy_transform.txt
Giorgos,
I have installed the FieldTrip toolbox associated with megconnectome 3.0, that
is fieldtrip-r10442. I
ut I do not know how to do
that.
-Jeff
From: Michalareas, Giorgos [mailto:giorgos.michalar...@esi-frankfurt.de]
Sent: Tuesday, February 14, 2017 3:03 PM
To: K Jeffrey Eriksen
Cc: hcp-users@humanconnectome.org
Subject: RE: [HCP-Users] MEG_anatomy_transform.txt
Hi Jeff,
there no need to run th
=[];
transform.vox07mm2spm = [
-0.7 0 0 90.7
0 0.7 0 -126.7
0 0 0.7 -72.7
0 0 0 1
]; % This is the transformation matrix you read with ft_read_mri from the
processed MRI file
transform.vox07mm2bti =vox07mm2spm;
transformfile=_MEG_anatomy_transform.txt
hcp_write_ascii (transformfile,'tran
iles and found no occurrence of
the transforms above, so they must be embedded in the shell scripts or compiled
C code somewhere, presumably.
Can you comment on the above and perhaps point me in the right direction? One
idea I have is to try to run the HCP-MEG pipeline minus the actual MEG
portio
the "analysis_functions" subfolder called
"hcp_write_ascii.m"
simply as
transformfile=_MEG_anatomy_transform.txt
hcp_write_ascii (transformfile,'transform');
and
I believe that should do it.
Give it a try and let me know if it worked or not .
It might be of interest to
Hi,
I am trying to import HCP processed data into Brainstorm, a Matlab-based
package for EEG/MEG source analysis, in order to build an EEG source model. I
do not work with MEG.
Unfortunately I am failing since I do not have the
_MEG_anatomy_transform.txt file that is created during the HCP-MEG
Hello,
I am a very new HCP Connectome WB user trying to import nifti and gifti files
into Brainstorm (Bst) for EEG modeling. I am having a strange problem and am
looking for some direction. In the past I was able to import T1.nii volume
files and lh.pial/rh.pial files from FreeSurfer with no pr
Hi,
I am a very new user of the workbench. I noticed the availability of the
Workbench Command and went to its home page. The example there shows Operating
System: Linux. Is it not available for WindowsOS? Is it for MacOS?
Thanks,
-Jeff
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