Hello. I am attempting to run fslvbm_2_template using a custom grey matter template built for my cohort of subjects. When I run the fslvbm steps without any alterations everything works fine, ie outputs are correctly generated. My population is younger and thus I am trying to use a custom general template (prior) and atlas. When I change the T= field from fsl/standard to the location of my template (which is .nii format) fslvbm_2 runs without any errors generated but there are files missing in the final /struc directory. I tried fslchfiletype to switch my template to analyze as the provided template was in .hdr .img format with no change in results. The missing files are:
*_GM_to_template_GM_init.log
*_GM_to_T_init_warp.nii.gz
*_GM_to_T_init.nii.gz (this file began showing up once I altered the $REG variable in the echo fsl_reg (nonlinear) to -a)
all the template_* files are created (probably from the first fsl_reg step in vbm_2 and I checked their alignment. The alignments are good and the _flipped is indeed flipped on the x axis but I don't think the program is running the fnirt process under fsl_reg.
Originally I was using a cohort of 6 controls and 6 others, but I have reduced that to 1 and 1 in order to decrease run times for testing. The segmentations from fast in vbm_2_template look good too.
Any ideas why the -n (nonlinear) step of fsl_reg would be failing in fslvbm_2_template and not produce any error message outputs? I read many similar questions on the message board but could not find any with a resolution that reflected the problems I am having (mainly because I don't get any error messages).
Thanks for any and all help.
Joseph
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