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Thanks for the support John! Orienting all the functional and structural images worked well! It also seemed that using the provided skull-stripped version led to a bad coregistration and normalization. After using the non skull-stripped version, all worked fine. I was under the impression that using skull-stripped structurals normally works better, but not in this case ;) greetings David 2017-03-28 15:41 GMT+02:00 John Ashburner <[log in to unmask]>: > My guess is that the segmentation worked (almost - the overly tight skull > stripping means the result is not perfect) after reorienting, but the > coregistration failed. Try also manually reorienting the fMRI (not just > the first volume, but all volumes within the 4D file). > > Best regards, > -John > > > On 28 March 2017 at 14:14, David Hofmann <[log in to unmask]> wrote: > >> Hi John, >> >> I thought so too, but after manually reorienting the T1 to the MNI >> template I get the same error and I have no clue what the problem is. Do >> you or others maybe have any other ideas how to find the cause of the >> problem? >> >> I attached a link to download the data (original, not reoriented by me). >> The subject is from the Bangor dataset of the 100 fcp, see: >> https://www.nitrc.org/frs/shownotes.php?release_id=820. >> >> here is the link: https://www.dropbox.com/s/mxsn >> h0fvj971f9r/sub87568_copy.zip?dl=0 >> >> greetings >> >> David >> >> >> 2017-03-23 11:01 GMT+01:00 John Ashburner <[log in to unmask]>: >> >>> As usual, my best guess is that the positioning information in the image >>> header is corrupt. I'd suggest trying a CheckReg between your image and >>> the MNI-space templates released with SPM. If the images are not within >>> about 4cm and 15 degrees of each other, you should adjust the positioning >>> information in the image header. >>> >>> Best regards, >>> -John >>> >>> >>> On 22 March 2017 at 16:57, David Hofmann <[log in to unmask]> >>> wrote: >>> >>>> Hi, >>>> >>>> I get the following error during segmentation and I'm not sure what the >>>> problem is. It seems the input to the SVD consists only of NaNs: >>>> >>>> >>>>> >>>>> SPM12: spm_preproc_run (v6365) 23:42:13 - >>>>> 21/03/2017 >>>>> ============================================================ >>>>> ============ >>>>> Segment X:\sub87568\mprage_skullstripped.nii >>>>> Warning: Matrix is singular to working precision. >>>>> > In spm_get_closest_affine at 61 >>>>> In spm_preproc_write8 at 337 >>>>> In spm_preproc_run>run_job at 146 >>>>> In spm_preproc_run at 41 >>>>> In spm_cfg_preproc8>spm_local_preproc_run at 418 >>>>> In matlabbatch\private\cfg_run_cm at 29 >>>>> In cfg_util>local_runcj at 1688 >>>>> In cfg_util at 959 >>>>> In spm_jobman>fill_run_job at 458 >>>>> In spm_jobman at 247 >>>>> >>>> >>>> >>>>> Failed 'Segment' >>>>> Error using svd >>>>> Input to SVD must not contain NaN or Inf. >>>>> In file "..\spm12\spm_get_closest_affine.m" (v6137), function >>>>> "spm_get_closest_affine" at line 68. >>>>> In file "\spm12\spm_preproc_write8.m" (v6881), function >>>>> "spm_preproc_write8" at line 337. >>>>> In file "\spm12\spm_preproc_run.m" (v6365), function "run_job" at line >>>>> 146. >>>>> In file "\spm12\spm_preproc_run.m" (v6365), function "spm_preproc_run" >>>>> at line 41. >>>>> In file "\spm12\spm12\config\spm_cfg_preproc8.m" (v6798), function >>>>> "spm_local_preproc_run" at line 418. >>>>> >>>> >>>> Additionally, there is a warning during coregistration which might be >>>> related to this: >>>> >>>> >>>>> SPM12: spm_coreg (v6435) 23:29:07 - >>>>> 21/03/2017 >>>>> ============================================================ >>>>> ============ >>>>> Warning: Too many optimisation iterations >>>>> > In spm_powell at 46 >>>>> In spm_coreg at 149 >>>>> In spm_run_coreg at 22 >>>>> In matlabbatch\private\cfg_run_cm at 29 >>>>> In cfg_util>local_runcj at 1688 >>>>> In cfg_util at 959 >>>>> In spm_jobman>fill_run_job at 458 >>>>> In spm_jobman at 247 >>>> >>>> >>>> Does anybody have an idea what went wrong and how to fix it? >>>> >>>> greetings >>>> >>>> David >>>> >>>> >>> >> >