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help > RE: Error using conn_process (line 554)
Mar 7, 2017 01:03 AM | Alfonso Nieto-Castanon - Boston University
RE: Error using conn_process (line 554)
Dear Jeremy,
That is strange indeed, the grey matter image and normalization results look perfectly fine. The error indicates that no voxels in your gray matter image have posterior probability values above 0.5, which is somewhat strange judging from the quality of the displayed mask. Could you please, within the SPM display, right-click on the image and select 'display intensities', and double-check whether in fact it appears that all values are below 0.5? Alternatively please mail me the wc1cbrain.nii image for the FD_0343 subject and I will take a quick look to see if that helps me figure out what might be the issue
Thanks
Alfonso
Originally posted by Jeremy Hogeveen:
That is strange indeed, the grey matter image and normalization results look perfectly fine. The error indicates that no voxels in your gray matter image have posterior probability values above 0.5, which is somewhat strange judging from the quality of the displayed mask. Could you please, within the SPM display, right-click on the image and select 'display intensities', and double-check whether in fact it appears that all values are below 0.5? Alternatively please mail me the wc1cbrain.nii image for the FD_0343 subject and I will take a quick look to see if that helps me figure out what might be the issue
Thanks
Alfonso
Originally posted by Jeremy Hogeveen:
Dear Alfonso and CONN experts,
I'm running into this same issue in CONN v.17. Here is the specific error message I receive when I run my conn batch:
Error using conn_process (line 610)
No suprathreshold voxels in ROI file /nfs/popasd/CoCoA/RiSE/fsl_analysis/fD_0343/anatomy/wc1cbrain.nii (this typically indicates a problem during normalization/segmentation for this subject; please try re-running normalization/segmentation step after manually re-aligning the structural volumes to better match the default template orientation)
Based on this thread, I checked the coregistration for the anatomical volume which looks nice (attached), as well as the grey matter image itself (also attached). My guess is that there is something wrong with the tissue segmentation, and I'm wondering if there are any suggested workarounds for this issue?
Any advice much appreciated!
Cheers,
Jeremy
I'm running into this same issue in CONN v.17. Here is the specific error message I receive when I run my conn batch:
Error using conn_process (line 610)
No suprathreshold voxels in ROI file /nfs/popasd/CoCoA/RiSE/fsl_analysis/fD_0343/anatomy/wc1cbrain.nii (this typically indicates a problem during normalization/segmentation for this subject; please try re-running normalization/segmentation step after manually re-aligning the structural volumes to better match the default template orientation)
Based on this thread, I checked the coregistration for the anatomical volume which looks nice (attached), as well as the grey matter image itself (also attached). My guess is that there is something wrong with the tissue segmentation, and I'm wondering if there are any suggested workarounds for this issue?
Any advice much appreciated!
Cheers,
Jeremy
Threaded View
| Title | Author | Date |
|---|---|---|
| Maxi Becker Becker | Jan 5, 2015 | |
| Kasey Hemington | Oct 2, 2015 | |
| Alfonso Nieto-Castanon | Oct 8, 2015 | |
| Jeremy Hogeveen | Mar 6, 2017 | |
| Alfonso Nieto-Castanon | Mar 7, 2017 | |
| Jeremy Hogeveen | Mar 7, 2017 | |