Dear Matt,
NaNs in the data sometimes and grayordinates with a constant timeseries in the
dense timeseries data were being introduced by mri_convert and using dcm2nii
fixes the issue, so the problem was not the extensive temporal preprocessing. I
wanted to share this finding just in case anyone else experiences this issue
too.
Best wishes,
Leah
From: Leah Moreno <mmorenoort...@icloud.com>
Date: Wednesday, May 17, 2017 at 5:56 PM
To: "Glasser, Matthew" <glass...@wustl.edu>, "hcp-users@humanconnectome.org"
<hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] NaNs and grayordinates with constant timeseries
Thank you for your prompt response.
Yes, this is whole brain data with full coverage of the CIFTI grayordinates
space. I have not tried just running the HCP minimal preprocessing pipelines
and ICA+FIX cleanup.
From: "Glasser, Matthew" <glass...@wustl.edu>
Date: Wednesday, May 17, 2017 at 5:50 PM
To: Leah Moreno <mmorenoort...@icloud.com>, "hcp-users@humanconnectome.org"
<hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] NaNs and grayordinates with constant timeseries
Do you have those issues if you just run the HCP minimal preprocessing
pipelines and ICA+FIX cleanup? I am guessing the issue lies with the
extensive temporal preprocessing that you are doing and not with the wb_command
-cifti-average-roi-correlation command or the CIFTI grayordinates themselves.
Is this whole brain data with full coverage of the CIFTI grayordinates space?
Peace,
Matt.
From: <hcp-users-boun...@humanconnectome.org> on behalf of Leah Moreno
<mmorenoort...@icloud.com>
Date: Wednesday, May 17, 2017 at 4:36 PM
To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: [HCP-Users] NaNs and grayordinates with constant timeseries
Dear experts,
I have run the HCP pipeline w/o errors. However, for a few patients the
functional connectivity maps are empty, i.e. the correlation fitting routine
does not converge for any region of the brain.
The command I use is: wb_command -cifti-average-roi-correlation
${basedir}/${idfolder}/${idfolder}_FCmap_from_seed.dscalar.nii -cifti-roi
seed.dscalar.nii –cifti ${basedir}/${idfolder}
RS_fMRI_1_Atlas_x4_mov_regr_b_lt_resid_brain_regr_resid_frcintrp_bpss_lc800_hc2.dtseries.nii
There are NaNs in the data sometimes. And in the dense timeseries data, there
are grayordinates with a constant timeseries. How can I solve this problem?
Thank you very much in advance.
Best wishes,
Leah Moran
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