When I do the third step, I now get the error:
ERROR: roi column is empty
The first command:
wb_command -cifti-separate 30_min.dtseries.nii COLUMN -volume AMYGDALA_LEFT
output_left_amygdala.nii.gz -roi roi_left_amygdala.nii.gz
The second command:
wb_command
That was the problem - sorry about that. I have extracted the mean time series
for the left amygdala now.
Thanks so much for the help!
I have one final question:
I assume that this ROI is from the freesurfer subcortical segmentation?
From: Timothy
I believe that was part of the process, however in order to get a standard
set of grayordinates across subjects, many subjects' segmentations were
combined to make an atlas parcellation. The minimal preprocessing
pipelines paper has some related information, but I'm not sure it covers
how the
Your second command is different than the one I posted - specifically, the
-volume option to -cifti-create-dense-from-template has a bug in v1.1 and
v1.1.1, which causes it to do the wrong thing even when it doesn't error,
use -volume-all instead (which does not take a structure name).
Tim
On
That is a bug in -cifti-create-dense-from-template we hadn't caught,
sorry. To work around it, you can remove the -crop option from the
-cifti-separate command (warning, may use a lot of memory, you could take
only the first frame with -cifti-merge before doing -cifti-separate, as for
this method
Hi Tim,
When doing the second step (turn the ROI into cifti), I get the following error:
ERROR: input volume doesn't match volume space and dimensions in CIFTI
The code I am using for the first step:
wb_command -cifti-separate 30_min.dtseries.nii COLUMN -volume AMYGDALA_LEFT
Hi Michael,
Thinking about this a little more, the differing phase encoding direction between your SE and BOLD fMRI is going to definitely be a problem, since the pipeline only has a parameter for a single "unwarp" direction. But, it would need separate UnwarpDir variables
for your
