Thanks a lot. Best regards, Amirhossein Manzouri
On Mon, Feb 17, 2014 at 4:54 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > they are automatically detected, but sometimes they can be too permissive > (or restrictive) in some regions in some acquisitions. If you look through > the recon-all.log file in your subject's scripts dir you can see what they > are set to (search for mris_make_surfaces), then look at where the surfaces > are wrong and see if you think changing some of the thresholds would help. > It will say something like: > > computing class statistics... > border white: 238722 voxels (1.42%) > border gray 265205 voxels (1.58%) > WM (101.0): 100.4 +- 7.9 [70.0 --> 110.0] > GM (76.0) : 75.1 +- 10.0 [30.0 --> 110.0] > setting MIN_GRAY_AT_WHITE_BORDER to 61.0 (was 70) > setting MAX_BORDER_WHITE to 113.9 (was 105) > setting MIN_BORDER_WHITE to 71.0 (was 85) > setting MAX_CSF to 50.9 (was 40) > setting MAX_GRAY to 98.1 (was 95) > setting MAX_GRAY_AT_CSF_BORDER to 66.0 (was 75) > setting MIN_GRAY_AT_CSF_BORDER to 40.9 (was 40) > > > and you can change any of them with expert options (look in the recon-all > --help). > > > cheers > Bruce > > > On Mon, 17 Feb 2014, amirhossein manzouri wrote: > > Thanks Bruce for the prompt reply. Would you please explain how can I >> control mris_make_surfaces parameters, is this a part of recon-all >> process? >> >> Best regards, >> Amirhossein Manzouri >> >> >> >> >> >> On Mon, Feb 17, 2014 at 3:35 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> Hi Amirhossein >> >> it's hard to tell without looking at the data, but you could try >> using the expert options to change the allowable intensity >> ranges for the different surfaces (e.g. if the white is too far >> out, don't allow mris_make_surfaces to put the gray/white border >> at intensities that are that dark) >> >> cheers >> Bruce >> >> >> On Mon, 17 Feb 2014, amirhossein manzouri wrote: >> >> Hi all, >> There is incorrect pial surface lines (red and >> yellow) in the right >> hemisphere of some of my subjects. The white matter >> and grey matter are very >> close regarding intensity and this can be seen in >> just a few slices and then >> it gets correct. I tried control points but >> regarding the low intensity they >> can be effective. I wonder if there is a way to >> correct this, or if they may >> affect the qdec analysis between group afterwards a >> lot.(since they are >> present in one or few slices and create thick GM in >> those slices!) >> >> Best regards, >> Amirhossein Manzouri >> >> >> >> >> >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> >>
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