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Dear SPM list,

We are trying to create a vdm file using the presubstracted phase and magnitude data option in SPM, to be used when running realign and unwarp. This works fine for all of the subjects except 1 where we get the error message:

Running 'Presubtracted Phase and Magnitude Data'
Segmenting and extracting brain...
Failed  'Presubtracted Phase and Magnitude Data'
Error using ==> schur
Input to SCHUR must not contain NaN or Inf.
In file "C:\Program Files\MATLAB\R2010a\toolbox\matlab\matfun\sqrtm.m" (???), function "sqrtm" at line 33.
In file "C:\toolbox\spm8\toolbox\FieldMap\pm_segment.m" (v4148), function "get_p" at line 580.
In file "C:\toolbox\spm8\toolbox\FieldMap\pm_segment.m" (v4148), function "run_segment" at line 363.
In file "C:\toolbox\spm8\toolbox\FieldMap\pm_segment.m" (v4148), function "pm_segment" at line 118.
In file "C:\toolbox\spm8\toolbox\FieldMap\pm_brain_mask.m" (v2616), function "pm_brain_mask" at line 48.
In file "C:\toolbox\spm8\toolbox\FieldMap\FieldMap.m" (v4571), function "FieldMap" at line 1625.
In file "C:\toolbox\spm8\toolbox\FieldMap\FieldMap_create.m" (v3670), function "FieldMap_create" at line 152.
In file "C:\toolbox\spm8\toolbox\FieldMap\FieldMap_Run.m" (v4571), function "FieldMap_Run" at line 134.
In file "C:\toolbox\spm8\toolbox\FieldMap\tbx_cfg_fieldmap.m" (v4571), function "fieldmap_presubphasemag" at line 766.

The following modules did not run:
Failed: Presubtracted Phase and Magnitude Data

We have checked all of the subjects' files to make sure that there is the correct number of them and that they are the same file size as the other subjects, where this method works. We have also tried using DICOM import again on the raw data. We are able to realign and unwarp without the vdm file for this subject, but since we are using the vdm for everyone else it is not ideal. Does anyone know why we are getting this error message and how we could fix it?

Thank you in advance for your help,

Patricia

--
Ms Patricia Lockwood
MRC DTA PhD student

Institute of Cognitive Neuroscience
Alexandra House, 17 Queen Square
London, WC1N 3AR

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