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Dear Christian, dear SPMers, I checked the image orientation (and just from comparing with the templates it looked similar) of my MP2Rage data files and set the origin to the anterior commissure. However, SPM still wants me to check the image orientation. I also attached the error report. Failed 'CAT12: Segmentation' Error using cat_main_gintnorm (line 347) Bad SPM-Segmentation. Check image orientation! In file "/afs/cbs.mpg.de/software/spm/12.6470/8.6/precise/toolbox/cat12/cat_main_gintnorm.m" (v882), function "cat_main_gintnorm" at line 347. In file "/afs/cbs.mpg.de/software/spm/12.6470/8.6/precise/toolbox/cat12/cat_main.m" (v889), function "cat_main" at line 567. In file "/afs/cbs.mpg.de/software/spm/12.6470/8.6/precise/toolbox/cat12/cat_run_job.m" (v887), function "cat_run_job" at line 519. In file "/afs/cbs.mpg.de/software/spm/toolboxes/cat12/0.890/cat_run.m" (v890), function "run_job" at line 210. In file "/afs/cbs.mpg.de/software/spm/toolboxes/cat12/0.890/cat_run.m" (v890), function "cat_run" at line 119. No executable modules, but still unresolved dependencies or incomplete module inputs. The following modules did not run: Failed: CAT12: Segmentation Skipped: Apply deformations (many images) Skipped: Move/Delete Files Failed 'Segment longitudinal data' Error using MATLABbatch system Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message) ------------------ Running job #3 ------------------ The following modules did not run: Failed: Segment longitudinal data Thanks a lot in advance for your help. Best, Elisabeth ----- Original Message ----- From: "christian" <[log in to unmask]> To: [log in to unmask], "Elisabeth Kaminski" <[log in to unmask]> Cc: "christian" <[log in to unmask]> Sent: Tuesday, March 15, 2016 3:08:53 PM Subject: Re: cat12 longitudinal tlbx processing Dear Elisabeth, sorry my fault. I haven't seen that you already attached this error. Best, Christian On Tue, 15 Mar 2016 14:16:07 +0100, Elisabeth Kaminski <[log in to unmask]> wrote: >Dear Christian, > >I am very sorry. Potentially, I posted my error message in the wrong folder: > >https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1603&L=spm&F=&S=&X=164C8BD1E198CE1FFF&Y=ekaminski%40cbs.mpg.de&P=185246 >This is where I attached my first error message. > >I will try to check out my file orientation and let you know if it works. > >Thanks a lot & sorry again. >Elisabeth > > > >----- Original Message ----- >From: "christian" <[log in to unmask]> >To: [log in to unmask], "Elisabeth Kaminski" <[log in to unmask]> >Cc: "christian" <[log in to unmask]> >Sent: Tuesday, March 15, 2016 2:03:39 PM >Subject: Re: cat12 longitudinal tlbx processing > >Dear Elisabeth, > >On Tue, 15 Mar 2016 11:08:59 +0100, Elisabeth Kaminski <[log in to unmask]> wrote: > >>Dear Helmut, >> >>thats right. So in this case: >> >>cat12.opts.biasreg = inf >>cat12.opts.biasfwhm = inf seems reasonable to me. >Again, even for the MP2RAGE images I would first try the default settings for bias correction. If there is no bias field there will be no correction. Furthermore, even MP2RAGE images still might be affected by small inhomogeneities that can influence segmentation accuracy. Thus, I would not completely skip this important step. > >> >>Is that what you are suggesting to obtain a weaker bias correction? >> >>Unfortunately, also the release of the new version of the cat12 toolbox (r890) still did not resolve my error. The toolbox still does not output any segmented images but skips that step and only produces an avg image and the rXXX images. Is there anything else, I could try? >> >>that is the error message in the MATLAB command window: >> >>Failed 'CAT12: Segmentation' >>Error using cat_main_gintnorm (line 347) >>Bad SPM-Segmentation. Check image orientation! >>In file "/afs/cbs.mpg.de/software/spm/12.6470/8.6/precise/toolbox/cat12/cat_main_gintnorm.m" (v882), function "cat_main_gintnorm" at line 347. >>In file "/afs/cbs.mpg.de/software/spm/12.6470/8.6/precise/toolbox/cat12/cat_main.m" (v889), function "cat_main" at line 567. >>In file "/afs/cbs.mpg.de/software/spm/12.6470/8.6/precise/toolbox/cat12/cat_run_job.m" (v887), function "cat_run_job" at line 519. >>In file "/afs/cbs.mpg.de/software/spm/toolboxes/cat12/0.890/cat_run.m" (v890), function "run_job" at line 210. >>In file "/afs/cbs.mpg.de/software/spm/toolboxes/cat12/0.890/cat_run.m" (v890), function "cat_run" at line 119. >> >>No executable modules, but still unresolved dependencies or incomplete module inputs. > >Uups, this is the first time that you mentioned and posted an error message regarding your issue. Without knowing that an exact error occurs I can't help. Please, always send full error messages, otherwise it is damn hard to help... > >Regarding this error message: Please follow that advice in the error message and check your image orientation. If images are in the correct SPM orientation (compare orientation with the templates in the spm12/canonical folder), then I would suggest to set the origin of your images before calling CAT12. Use the Display function for that purpose, roughly set the origin (anterior commissure) and press the "set Origin" button to apply this correction. > >Best, > >Christian > >> >>I also attached the error report that I got from SPM. >> >>Thank you very much for your continuous help on these issues! >> >>Best, >>Elisabeth >> >> >>----- Original Message ----- >>From: "MRI More" <[log in to unmask]> >>To: [log in to unmask], "Elisabeth Kaminski" <[log in to unmask]> >>Sent: Monday, March 14, 2016 6:45:22 PM >>Subject: Re: cat12 longitudinal tlbx processing >> >>Dear Elisabeth, >> >>> very light bias regularisation >>You would want to go the opposite, more extreme regularisation to obtain a weaker bias correction. >> >>Best >> >>Helmut