That is the "cost" of the registration. You can look in Greve & Fischl
2009 to see how it is computed.
doug
On 2/9/15 3:45 PM, sabin khadka wrote:
Hi Doug- Works fine. I appreciate your help.
Related but different question: Would you help me understand how the
QA value(0-1)while checking registration using following command is
calculated.
tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum
Cheers,
Sabin Khadka
------------------------------------------------------------------------
*From:* Douglas Greve <gr...@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
*Sent:* Monday, February 9, 2015 3:32 PM
*Subject:* Re: [Freesurfer] time series data from FSFAST
On 2/9/15 3:16 PM, sabin khadka wrote:
Thanks Doug. I am now able to get average time series from cortical
ROIs. I used
mri_segstats --annot fsaverage lh aparc --i
sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt
That's right, but I would use the unsmoothed data since smoothing will
cause activity to spill-over between regions.
How would I get time series of the sub-cortical ROIs
(fmcpr.up.sm5.mni305.2mm.nii.gz)?
I tried doing
mri_segstats --seg fsaverage/mri/aseg.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt
but it gave me dimension mismatch error. I'd appreciate if you'd
direct me on how to get average time series values from subcortical
regions.
Use fsaverage/mri.2mm/aseg.mgz
doug
Cheers,
Sabin Khadka
------------------------------------------------------------------------
*From:* Douglas Greve <gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Monday, February 9, 2015 1:24 PM
*Subject:* Re: [Freesurfer] time series data from FSFAST
Yes, mri_segstats. Run it with --help. See esp example 6
On 2/9/15 12:31 PM, sabin khadka wrote:
Hi FS Users,
I've preprocessed resting state fmri data using preproc-sess as
shown in FSFAST functional connectivity walk through manual. I know
I can extract mean time series of a seed region using fcseed-sess. I
am trying to find a command to extract mean time series from all
Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the
command to get the time-series of all the ROIs at once in a .txt or
.dat files but I am not sure how exactly to do it.
Thanks for help.
Cheers,
Sabin Khadka
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