Re: [Freesurfer] mri_watershed and improvements of skullstripping

2023-08-05 Thread Michelangelo Fabbrizzi 
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I have to add a last question:
3- how can I generate the -head.fif file from the surfaces I have created 
(brain_surface, inner_skull_surface corrected with 1mm, outer_skull_surface 
corrected with -2mm, outer_skin_surface)? I should then use them in MNE

Greatly appreciated!


> Il giorno 5 ago 2023, alle ore 17:33, Michelangelo Fabbrizzi 
>  ha scritto:
> 
> 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 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> External Email - Use Caution
>> 
>> 
>> 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:
>>> External Email - Use Caution
>>> 
>>> 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 
>>> 
>>> Your help is greatly appreciated!
>>> 
>>> Michelangelo
>>> 
 Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing 
   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-boun...@nmr.mgh.harvard.edu 
  
  
  On Behalf Of Michelangelo 
 Fabbrizzi
 Sent: Sunday, July 30, 2023 9:32 AM
 To: freesurfer@nmr.mgh.harvard.edu 
 ; fsbuild  
 ; freesurfer-ow...@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

[Freesurfer] Question about group analysis

2023-08-05 Thread inbal paran 
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Hello FreeSurfer Developers,

I have a question regarding group analysis:
When I followed the instructions on how to build my FSGD file,
it said that:"FSGD files are created automatically by qdec, but qdec
is currently (12/9/08)
limited to two continuous variables and two discrete variables with two levles.
Is this still the case, or is it possible to include more than 2
continuous variables?

The freesurfer version I am using:
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

Thank you
Inbal


-- 

*Inbal Paran, M.PT 
.*
Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy
Department, Recanati School for Community Health Professions.
Faculty of Health Sciences at Ben-Gurion University of the Negev.
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[Freesurfer] How to compute the merged volume of both hemispheres per each ROI

2023-08-05 Thread inbal paran 
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Hello FreeSurfer Developers,

I need to compute the volume of specific bilateral cortical and
subcortical ROIs.
I already ran reacon-all on all of my subjects, and I extracted
volumes of the ROIs
per hemisphere of both the cortical and subcortical brain regions
(aseg and aparc).

How can I compute the merged volume of both hemispheres per each ROI?

The freesurfer version I am using:
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

Thank you
 Inbal
-- 

*Inbal Paran, M.PT 
.*
Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy
Department, Recanati School for Community Health Professions.
Faculty of Health Sciences at Ben-Gurion University of the Negev.
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