[cclan]

Dear BrainSuite Experts,

I am running thicknessPVC.sh,
and it generated the following warning:
“Warning: Input tol may not be achievable by PCG
Try to use a bigger tolerance
> In pcg (line 88)
In thicknessPVC (line 159)

ans =

1.0e+03 *

0.0030 0.0000 2.7280
”

What does it mean in terms of the results and output files it generated?
What should I do to solve this problem?

Thank you very much!

Best regards,
Chen-Chia

[Anand Joshi]

Most likely this is due to processing error at earlier stages.
Can you check if your extracted brain surfaces look realistic?

[cclan]

Hi

Which one of the output files would be best to look at?

Thank you very much!

[Anand Joshi]

You can check *left.inner.cortex.dfs, *right.inner.cortex.dfs
*left.pial.cortex.dfs, *right.pial.cortex.dfs

[cclan]

Hi

The *left.inner.cortex.dfs and *right inner cortex.dfs were all grey and looks OK, the pial.cortex.dfs are mostly red wit blue patches over occipital pole, fusiform gyri and OFC and the contour looks fine.
However, the atlas.pvc-thickness_0-6mm.right.mid.cortex.dfs and atlas.pvc-thickness_0-6mm.leftt.mid.cortex.dfs were on the surface with contour similar to atlas.right.mid.cortex.jacobian.dfs and atlas.left.mid.cortex.jacobian.dfs unlike the ones in the ICBM tutorial output folders.

Thank you!

[Anand Joshi]

Can you share the screenshots if possible? You can use dropbox links for example.

[Anand Joshi]

Also, since you see atlas.pvc-thickness_0-6mm.right.mid.cortex.dfs and atlas.pvc-thickness_0-6mm.left.mid.cortex.dfs
the execution of cortical thickness script seems to have finished.

[cclan]

Hi Professor Joshi

Is your email ajoshi@sipi.usc.edu?
Perhaps I could send you a dropbox link via email of one of the subject folder I processed on my college HPC with cortical_extraction.sh, svreg.sh, and thicknessPVC.sh?
The subjects’ folder all showed stagnation of the PCG function in thicknessPVC.sh.

Thank you very much!

Best regards,
Chen-Chia

[cclan]

Hi professor Joshi

Would it be possible for you to kindly take a look at my thicknessPVC processed files, especially the out put of thicknessPVC, the atlas.pvc-thickness_0-6mm.right.mid.cortex.dfs and atlas.pvc-thickness_0-6mm.leftt.mid.cortex.dfs, etc. to see if they are processed correctly?

If it is OK, I will send a processed folder via dropbox link to your email, ajoshi@usc.edu ?

Thank you very much!

Best wishes,
Chen-Chia

[Anand Joshi]

Sure, please send a dropbox link to ajoshi@usc.edu or ajoshi@sipi.usc.edu and I will take a look.
Thank you, best, Anand

[Author]

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