Hi,

When calling recon-all autorecon3, with the -T2pial flag, and a -T2_min value specified via expert options file, I noticed that this parameter is passed to the first call of mris_make_surfaces, which looks, for example, as follows:

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#@# Make Pial Surf lh Mon Aug 19 13:43:02 CEST 2019

<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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#@# Refine Pial Surfs w/ T2/FLAIR Mon Aug 19 14:02:23 CEST 2019

<other T2 pial steps>

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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Is this the expected behavior, or should the T2_min be passed to the second call as well? In case it is needed, I am using freesurfer-dev, version obtained on july 11th. Thank you very much.

Best,

Marco