HCPpipeline error
lei wei
Hi HCP expert,
I am trying to run the HCP structural pipeline in LegacyStyleData mode, but the processing fails in the FreeSurfer step due to a missing surface file surf/lh.white.preaparc.rawavg.
From the recon-all/FreeSurferPipeline log, I see the following:
INFO: trgsubject = srcsubject
Saving target data
Computing bias field from rawavg
mri_normalize -sigma 8 -erode 1 -min_dist 1 \
-surface ../surf/lh.white.preaparc.rawavg identity.nofile \
-surface ../surf/rh.white.preaparc.rawavg identity.nofile \
rawavg.cmdc.mgz rawavg.norm.mgz
using Gaussian smoothing of bias field, sigma=8.000
eroding interior of surface 1 times
retaining nonmaximum suppressed points that are at least 1.000mm from the boundary
reading mri_src from rawavg.cmdc.mgz...
Copying mri_dst from mri_src
error: No such file or directory
error: MRISread(../surf/lh.white.preaparc.rawavg): could not open file
error: mri_normalize: could not surface ../surf/lh.white.preaparc.rawavg
However, I do see a file named white.preaparc.rawavg under the mri/ directory and the lh.white.preaparc can also be found at surf folder. I using FS 7.4.1 to run HCPpipeline and no T2w image as input.
Could you please to let me know how to resolve this error ？
Really appreciate for any help!
lei
Glasser, Matthew
FS greater than 6.0 is not currently supported. We are working on it.
Matt.
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