BrainSuite

thicknessPVC warning? Help please! Thank you.

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    • November 13, 2018 at 10:03 am #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?

      • November 13, 2018 at 10:25 am #1540
        cclan
        Participant

          Hi

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

          Thank you very much!

        • November 13, 2018 at 11:55 am #1541
          Anand Joshi
          Moderator

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

          • November 13, 2018 at 1:20 pm #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!

            • November 13, 2018 at 1:41 pm #1543
              Anand Joshi
              Moderator

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

              • November 13, 2018 at 1:42 pm #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.

                • November 13, 2018 at 2:02 pm #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

                  • November 15, 2018 at 6:21 am #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

                    • November 15, 2018 at 10:37 am #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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