Re: [HCP-Users] MEG-source template model of 8004 vertices

Hi Ola, You will find some templates in https://github.com/Washington-University/megconnectome: its template folder contains some *4k* surface giftis (midthickness and inflated). As a side note, the source meshes are not in MNI space,

Re: [HCP-Users] 答复: 答复: About wb_command -cifti-resample

REA and CUBIC (cubic > spline), except for label data which should use ADAP_BARY_AREA and > ENCLOSING_VOXEL. Using ADAP_BARY_AREA requires specifying an area > option > to each used -*-spheres option. > > The argument must be one of the following: > >

Re: [HCP-Users] 答复: About wb_command -cifti-resample

Hi Rigel, I don’t see why you want to resample it, nor why it needs to be converted into a cifti file. What’s your motivation for this? Best wishes, Jan-Mathijs > On 15 Jan 2019, at 15:55, Rigel Wang > wrote: > > Hi Prof. Jan-Mathijs, > Thank you for your fast reply, this is very useful, I

Re: [HCP-Users] About wb_command -cifti-resample

Hi Rigel, I suggest to use the low resolution subject-specific source models, which are part of the release data and are expressed in native space. They exist in a 4k and 8k vertex-per-hemisphere version. See page 92 of the S900 release manual. Best wishes, Jan-Mathijs > On 15 Jan 2019, at

Re: [HCP-Users] Freesurfer script

Hi Sara, These scripts are obsolete and not available in the release version of the megconnectome software. The FieldTrip website has a tutorial that achieves more or less the same thing as what you are aiming for:

Re: [HCP-Users] how to convert BTI space to MNI space

(i.e. the vertex positions) with the ones from the gifti-files. Best wishes, Jan-Mathijs > > > 发件人: hcp-users-boun...@humanconnectome.org > 代表 Jan Mathijs Schoffelen > > 发送时间: 2018年6月21日 13:05:13 > 收件人: hcp-users@humanconnectome.org > 主题: Re: [HCP-Users] how to co

Re: [HCP-Users] MEG TFLA possible misalignment ?

Hi Benjamin, The participants were asked to perform a sequence (10 in a row) of ‘rhythmic’ taps, cued by the visual flashes. My suspicion is that occasionally the subjects were anticipating the cue a bit too eagerly, getting ahead of the pacing stimulus now and then. Best wishes,

Re: [HCP-Users] how to convert BTI space to MNI space

Dear Felix, Could you try and explain why you think you need this conversion? The transformation to MNI space is a non-linear one, which invalidates any subsequent analyses on the MEG data. If you think you need it for visualization purposes, the transformation should also not be needed, since

Re: [HCP-Users] The plotting of HCP Resting state MEG data problem

Dear Felix, > When I was processing the data with the pipeline megconnectome-3.0, I found > that in the function hcp_datacheck, there is a code saying: hsname = > [dirname, '/hs_file']; But I did not find the hs_file in the raw data above. > Because I want to get the same or similiar figure

Re: [HCP-Users] RV: HCP resting-state MEG sensor position problem

Dear Felix, The coordinate system in which the channels are represented is ALS, the native coordinate system of the 4D system. >From the picture you pasted it seems that the software you use for >visualization makes some assumptions on the orientation of the X/Y/Z axis, >which ssems to be

[HCP-Users] Fwd: HCP-Users Digest, Vol 60, Issue 16

the list at > hcp-users-ow...@humanconnectome.org > <mailto:hcp-users-ow...@humanconnectome.org> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of HCP-Users digest..." > > > Today's Topics: &

Re: [HCP-Users] source MEG icablpenv projection

Dear Ola, You can directly average across subjects, no morphing is needed. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen,

Re: [HCP-Users] MEG Surface Parcellation

Dear Julia, If you want to parcellate the low-resolution (i.e. ~4k vertices per hemisphere) MEG source level time series, you first need to create the appropriate low-resolution dlabel file, sampled at 4k. The one you provided in your e-mail represents the parcellation at 32k vertices. This

Re: [HCP-Users] Source-MEG Resting state data

Dear Ola, The information you are looking for is described in the 900 Subjects Release reference manual (somewhere on page 93-104). The band-limited power envelopes at source level have been sampled at a frequency of approximately 50 Hz (i.e. one estimate per 20 ms). The restingstate runs

Re: [HCP-Users] need more information about warning: disabling cfg tracking

Yes, it can be safely ignored. More information can be found on: http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3187 Best , Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction

Re: [HCP-Users] hcp_anatomy.m needs an hsfile?

Hi Jeff, The hs_file is the MEG-system specific file format for a binary 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

Re: [HCP-Users] Transformation matrix (bti2spm)

Rikkert, Please check the MEG reference documentation. On page 30 it is mentioned that the dipole positions are indeed by construction not regularly spaced. If you want to have them in normalized space you will need to replace the subject specific source positions with the corresponding

Re: [HCP-Users] Missing T1w_acpc_dc_restore files

Hi Gregory, Although it is not clear to me why you would need the anatomical image when processing the MEG data - the coregistration information is provided in the MEG anatomy packages - the anatomicals you refer to (T1w_acpc_dc_restore.nii.gz) are available from the subjects’ MEG_anatomy

Re: [HCP-Users] ; MEG data, field trip analysis

Dear Jennifer, See my comments inline: I have used Morlet wavelets to analyze preprocessed MEG data from the HCP in resting state and the n-back working memory task. The input parameters that I have selected are as follows: cfg = []; cfg.channel= 'MEG';

Re: [HCP-Users] where are the head shape file for MEG

2015-05-15 22:09 GMT+02:00 jan-mathijs schoffelen jm.schoffe...@gmail.com: Hi Denis, Following up on my previous comment: why is it exactly you want the mapping to freesurfer space? The 123456_meg_anatomy_sourcemodel_2d.mat is already in helmet space. If you want to use it with MNE suite

Re: [HCP-Users] problems during coregistration with fiducials

are represented in the 100307_MEG_anatomy_transform.txt), what is it you want to do? Best wishes, Jan-Mathijs Jan-Mathijs Schoffelen, MD PhD Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging

Re: [HCP-Users] problems during coregistration with fiducials

-registred and I was able to do source analysis etc. What I wanted to do is to re-compute the sourcemodel warped in the aal-mni-space instead of mni-space as it is now. Many thanks tzvetan Best wishes, Jan-Mathijs Jan-Mathijs Schoffelen, MD PhD Max Planck Institute

Re: [HCP-Users] Fwd: Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen

for that command either? Best, Cherry On Sun, Mar 8, 2015 at 2:24 PM, jan-mathijs schoffelen jm.schoffe...@gmail.com wrote: Hi Cherry, Sorry about this. Could you go to the following URL and follow the instructions in order to create a ‘bug’ on FieldTrip’s bug tracking website: http

Re: [HCP-Users] Fwd: Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen

Hi Cherry, Sorry about this. Could you go to the following URL and follow the instructions in order to create a ‘bug’ on FieldTrip’s bug tracking website: http://fieldtrip.fcdonders.nl/bugzilla ? It would be great if you could create this bug and also upload the dense label file that is giving

Re: [HCP-Users] Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen

/ft_read_cifti.m Could you give it a try and report back whether this version of the code works for your purposes? Thanks and best wishes, Jan-Mathijs Jan-Mathijs Schoffelen, MD PhD Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands Donders Institute for Brain, Cognition