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Hi,

I would like to report a bug in freesurfer-dev. I have encountered this bug in a version downloaded on July 11th, 2019, and again in a version downloaded two days ago (August 20th). In short, it seems that parameters specified via an expert file relevant to T2-assisted pial segmentation, such as -T2_min, are not passed to the second call of mris_make_surfaces (the one actually using T2 data). 

In Freesurfer 6.0.0, this is not the case, and the T2_min parameter is indeed passed to the second call of mris_make_surfaces (although I note that in 6.0.0, when specifying -nsigma_below via the expert file, both the user-specified value and the standard value are passed to the second call of mris_make_surfaces). See below for more details on the specific freesurfer-dev behavior.

Best,

Marco Aqil

Bug description: T2-specific parameters not passed to second call of mri_make_surfaces in freesurfer-dev

Call: recon-all autorecon3​ -subjid <subject id> -hires -T2pial -parallel -openmp 15 -expert <expert file path>

Expert file content: mris_make_surfaces -T2_min 35

>From the recon-all log, the first call of mris_make_surfaces receives the -T2_min parameter:

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<scripts folder path>

mris_make_surfaces -save-res -save-target -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs -T2_min 35 sub-006 lh

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However, the second call of mris_make_surfaces, which relies on T2 data to refine the pial, does not receive the T2_min parameter, and looks as follows:

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mris_make_surfaces -save-res -save-target -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 sub-006 lh 

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I observed the same behavior when specifying -nsigma_below via the expert file.