thicknessPVC warning? Help please! Thank you.

Forums Forums Surface and Volume Registration (SVReg) thicknessPVC warning? Help please! Thank you.

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    • #1538
      cclan
      Participant

      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

    • #1539
      Anand Joshi
      Moderator

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

    • #1540
      cclan
      Participant

      Hi

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

      Thank you very much!

    • #1541
      Anand Joshi
      Moderator

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

    • #1542
      cclan
      Participant

      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!

    • #1543
      Anand Joshi
      Moderator

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

    • #1544
      Anand Joshi
      Moderator

      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.

    • #1545
      cclan
      Participant

      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

    • #1547
      cclan
      Participant

      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

    • #1550
      Anand Joshi
      Moderator

      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

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