I fully agree with Matt. This is our repeated experience with 'legacy' data
that we push through HCP pipelines. Taking cortical signals to the surface
results in major gains.
Best,
Alan
From: hcp-users-boun...@humanconnectome.org
Thanks Tim,
I’ll check for NaNs and try viewing in other viewers to make sure it’s not just
a thresholding thing. Will try other segmentations too, though the one I’m
using has full brain coverage, so I think the holes shouldn’t be caused by that.
Thanks for the help,
jared
> On Feb 23,
wb_command -file-information has a column with a count of inf/NaN values.
Since -fix-zeros has an effect, I suspect that some kind of thresholding is
going on in fsl_view, rather than the smoothing being the issue.
The volume parcel smoothing will output zero values anywhere that you don't
have
Thanks for the reply Tim,
I’m having trouble getting them to open in wb_view. Running out of memory even
when I request 60G, though the files themselves are 4.2G. There’s only 1
overlay in the red-yellow palette there and it’s overplayed over the
MNI152_T1_2mm template. I think it looks
Here are the commands run:
wb_command -volume-parcel-smoothing \
${subID}_concat4_rfMRI_REST_hp2000_clean_.nii.gz \
MNI152_T1_2mm_strucseg_label.nii.gz \
4 \
${subID}_concat4_rfMRI_REST_hp2000_clean_s4Parc_0.nii.gz \
-fix-zeros
wb_command -volume-smoothing \
Dear Matt,
Yes, I see the freesurfer pipeline fails, but i dont understand where
exactly the problem occurs . In FS2CaretConvertRegisterNonlinear.sh , The
problem occurs at the following lines of code.
#Find c_ras offset between FreeSurfer surface and volume and generate
matrix to transform
Dear all,
When i tried to run Freesurfer Pipeline i am facing an error where the
pipeline could not generate brain.finalsurfs.mgz . Could you please let me
know the reason for this error?.
START: FS2CaretConvertRegisterNonlinear
FreeSurfer2CaretConvertAndRegisterNonLinear.sh: RegName: MSMSulc
