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Dear Experts,

I reran -autorecon1 with the -expert option adding in the file xopts.txt:
mri_normalize -mprage -b 20 -n 5 -gentle \n mri_watershed -h 5 -atlas -useSRAS -surf sub-01_recon

This improved a lot the surfaces, however the inner_skull and outer_skull surfaces, are still crossing (I suspect this is due to the fact that I am using pediatric data and the shift of the surfaces are too big maybe?).

So I created a new inner_skull and outer_skull surfaces giving a shift of +1mm and -2mm respectively using Freesurfer commands:

mris_expand sub-01_recon_brain_surface 1 sub-01_recon_inner_skull_surface
mris_expand sub-01_recon_outer_skin_surface -2 sub-01_recon_outer_skull_surface

They are now much better, see attached screenshots (before shift correction and after it).

I would have two questions for you:

1- it looks the brainmask.mgz still contain three pieces of skull (see screenshot below)…is there any other way to remove them (-less removes too much)? better if from command line, otherwise even manual intervention

2- is it possible to force mri_watershed to use a smaller value of the shift when it generates the inner_skull and outer_skull surfaces from the brain_surfaces and outer_skin_surface (instead of using another command after it as I did with mris_expand)?

I greatly appreciate your help and thank you in advance for it!

Miche

Il giorno 1 ago 2023, alle ore 00:22, Douglas N. Greve <dgreve@mgh.harvard.edu> ha scritto:
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there are not options to autorecon1 specifically. You can pass some watershed args on the command line, but it is probably easier to use an expert options file, eg, create a text file (eg, xopts.txt) with something like
mri_watershed -less
then run recon-all with -expert xopts.txt (and the rest of your args)
You can add as many options as you want to that line

On 7/31/2023 1:22 PM, Michelangelo Fabbrizzi wrote:
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Dear Yujing,

thanks again for your help, just a last question, how can give to autorecon1 the input to use certain options at the mri_watershed step (for instance a certain preflood height (-h 5) or use of the atlas option (-atlas))?

recon-all -s sub-01_recon -i T1w.nii.gz -autorecon1 xxxx

Your help is greatly appreciated!

Michelangelo

Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing <YHUANG43@mgh.harvard.edu> ha scritto:

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I'm not sure how to force mri_watershed command to use the brainmask.mgz already created.

Recon-all '-gcut' is achieved by running mri_gcut after mri_watershed.

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 9:32 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild <fsbuild@contbay.com>; freesurfer-owner@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed and improvements of skullstripping

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Dear Freesurfer experts,

I am new to FS, and I would have couple of questions.
I used in sequence:
A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1
B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon
C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon

The brainmask.mgz obtained is good (no skull, brain is okay), however if I now use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not used and it is created a new one called ws.mgz that still contain some piece of skull that generate wrong BEM surfaces; even using -h 5 the result is not optimal:
mri_watershed -h 5 -useSRAS -surf /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon /Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz

I am wondering:
- how can I force the mri_watershed command to use the brainmask.mgz already created after step C above, instead of creating a new one?
- is it possible to use the -gcut command also for mri_watershed?

Thanks, appreciated,

Miche

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