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PS - I realize I forgot to mention that running fslview $FSLDIR/data/standard/tissuepriors/avg152T1_gray struc/template_GM demonstrated good alignment as well. On Wed, Sep 17, 2014 at 6:30 PM, Salil Soman <[log in to unmask]> wrote: > Dear Mark, > > Thank you for your response. The template_4D_GM.nii.gz file looked good, > and it contained all 64 volumes from my template_list file. > > Are there other files I should check to explain this error for step 3? > > Thank you for your consideration. > > Best wishes, > > Salil > > Date: Wed, 17 Sep 2014 18:02:44 +0000 > From: Mark Jenkinson <[log in to unmask]> > Subject: Re: fslvbm data mask is blank error for step 3 > > Hi, > > Have you checked that the outputs of steps 1 and 2 are correct? > It sounds like the problem with the mask is likely to be a symptom of a > problem earlier on. > > All the best, > Mark > > > > On 15 Sep 2014, at 08:07, Salil Soman <[log in to unmask]<mailto: > [log in to unmask]>> wrote: > > > Dear List Members, > > I have processed using data using steps 1 and 2 of fslvbm. When I run step > 3, 3A seems to complete properly, however 3 outputs an error file into the > stats directory stating that there was an error because the fslvbm data > mask is blank. If anyone could provide guidance on what is going wrong and > how to fix it, it would be greatly appreciated. > > Best wishes, > > Salil Soman, MD, MS > > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System