External Email - Use Caution
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
External Email - Use Caution
Dear All,
another question: after the below if I use the command to run autorecon2: recon-all -s sub-01_recon -autorecon2
I get the following error: ERROR: cannot find or read transforms/talairach.m3z
Can you help me please?
Thanks, regards,
Michelangelo
Il giorno 30 lug 2023, alle ore 15:32, Michelangelo Fabbrizzi michefabb@gmail.com ha scritto:
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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Hi Michelangelo,
I'm wondering if you are using FS 7.3.2? 'DOCAREG' was accidentally dropped for autonrecon2. You can fix it by adding '-careg' at the end of command line.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Michelangelo Fabbrizzi Sent: Sunday, July 30, 2023 11:34 AM To: freesurfer@nmr.mgh.harvard.edu; fsbuild fsbuild@contbay.com; freesurfer-owner@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use Caution Dear All,
another question: after the below if I use the command to run autorecon2: recon-all -s sub-01_recon -autorecon2
I get the following error: ERROR: cannot find or read transforms/talairach.m3z
Can you help me please?
Thanks, regards,
Michelangelo
Il giorno 30 lug 2023, alle ore 15:32, Michelangelo Fabbrizzi <michefabb@gmail.commailto:michefabb@gmail.com> ha scritto:
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
External Email - Use Caution
You don’t need ‘-careg’ if you just run autorecon3.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Michelangelo Fabbrizzi Sent: Monday, July 31, 2023 8:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use Caution Dear Yujing,
yes, I am using FS 7.3.2, so thanks I will try with
recon-all -s sub-01_recon -autorecon2 -careg
should I add the -careg also for the -autorecon3 step?
Can you eventually have a look also at the questions in my first email below (at the very bottom of this email trail)?
Greatly appreciated!
Il giorno 31 lug 2023, alle ore 14:51, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> ha scritto:
External Email - Use Caution Hi Michelangelo,
I’m wondering if you are using FS 7.3.2? ‘DOCAREG’ was accidentally dropped for autonrecon2. You can fix it by adding ‘-careg’ at the end of command line.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Michelangelo Fabbrizzi Sent: Sunday, July 30, 2023 11:34 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com>; freesurfer-owner@nmr.mgh.harvard.edumailto:freesurfer-owner@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use Caution Dear All,
another question: after the below if I use the command to run autorecon2: recon-all -s sub-01_recon -autorecon2
I get the following error: ERROR: cannot find or read transforms/talairach.m3z
Can you help me please?
Thanks, regards,
Michelangelo
Il giorno 30 lug 2023, alle ore 15:32, Michelangelo Fabbrizzi <michefabb@gmail.commailto:michefabb@gmail.com> ha scritto:
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ifXI2CrT6fdUd0Izxj6gRSO4lqIKipD6XZ2lWVS5fWo-1X... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1Vc9SOMD5QGa_ciVc0xydm7dUgGwJRUqQPnEQUMWTtlwYu7... https://secure-web.cisco.com/1Vc9SOMD5QGa_ciVc0xydm7dUgGwJRUqQPnEQUMWTtlwYu7BtmejcKKr8T8w9casBoBMISqVb-FCj4KTlm1p9FxUHuEttFBWw1Lc_KLV8Z2gIt-L9iziV2fnFZwzH0B92rMyjF6HAgKPPlUYC4GfjF3u4Je2NoMa14x_Rd8VlgDXt87-2AdWH1ZJ4n6en3e5yYjrPYvUYIjmHA3QcqSJFCUanSfgEvzuhIHhZiM6k76hola68md_NsqZId41trdcJ_oiIxlMhPdMz-7zOlkSb4w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
External Email - Use Caution
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
External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1cF5CFj8ObeEdVU_l8xNGBdbJJ0PpzQ0VrSp5AzRUYXgIxG...
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 xxxx
Your help is greatly appreciated!
Michelangelo
Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing YHUANG43@mgh.harvard.edu ha scritto: External Email - Use Caution
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
External Email - Use CautionDear 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1cF5CFj8ObeEdVU_l8xNGBdbJJ0PpzQ0VrSp5AzRUYXgIxG...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1cTHii2jK1prD_CnADwRM4fGIQbTqO7yHAtvDOSHvIUNYRG... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/19ZF3Eo2hejHW73PfG4iB-XcRcs7fDWd8GwCtm3h9M_CC3_... https://secure-web.cisco.com/19ZF3Eo2hejHW73PfG4iB-XcRcs7fDWd8GwCtm3h9M_CC3_u6UtvHsVzHGJ-1ZaDUpHru1S1350N_ophruGMIVTSUAv64GW-Hwy_XyWmghNedfA49x6wRn00_gB0ImsWecfgk-dZV6zDjqYm-SO-bvmNVa-Ef1VWLS5LsKI0Jg_XBgMJ5b732gLMmCbhfEKJSepG9O0C8raL9wICrMzY89GNBrSv7dTYxKxxdLKCUIzdyircSGYJ8bI-SXqUeemRvcRtOTWchnl6BVYrtEQhzg_HfULERNoDWNcgo6IVkMQt-6628n4GLwL1ikksBbpWBzc_8Slb_7LKNXneCZrN6oA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
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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:
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 xxxx
Your help is greatly appreciated!
Michelangelo
Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing YHUANG43@mgh.harvard.edu ha scritto:
External Email - Use Caution
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
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1cF5CFj8ObeEdVU_l8xNGBdbJJ0PpzQ0VrSp5AzRUYXgIxG...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/15k8N-Zo4AKDYaXF49SR8hi6D1Ts33kcqH2-zVmVVMdx_wY... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1lYbMeUuB3ZNZzX5_HF-RzuItvwTGVyuABaYThW437kw_ls... https://secure-web.cisco.com/1lYbMeUuB3ZNZzX5_HF-RzuItvwTGVyuABaYThW437kw_lsdMuaS3KofGAQlE1PXtnzXXCqtHc1eMhJYz6zonGfAznIJFJ-fKcKrm-fDUDU7pv4yRCwGP0IsrxUyqHOvTBIRm3Wcp56rC5t9tBdF5M3s3ukjZjLCOWvP7z5asuohDd51LZCHZ9Pj6rl-BqvXSHZU4WwsvodG1Qgg3DXBrRo3c0yhlt4bBmLdaYHFEiRemaqKiMinIlO_1KTqSjt0f/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/15k8N-Zo4AKDYaXF49SR8hi6D1Ts33kcqH2-zVmVVMdx_wY...
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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:
External Email - Use Cautionthere 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 CautionDear 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 mailto:YHUANG43@mgh.harvard.edu ha scritto:
External Email - Use CautionI'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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto:freesurfer@nmr.mgh.harvard.edu; fsbuild fsbuild@contbay.com mailto:fsbuild@contbay.com; freesurfer-owner@nmr.mgh.harvard.edu mailto:freesurfer-owner@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use CautionDear 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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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 michefabb@gmail.com 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). <Surfaces_without_shift_correction.png>
<Surfaces_with_shift_correction.png>
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
<Schermata 2023-08-05 alle 17.20.04.png>
Il giorno 1 ago 2023, alle ore 00:22, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> ha scritto:
External Email - Use Cautionthere 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 CautionDear 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 mailto:YHUANG43@mgh.harvard.edu ha scritto:
External Email - Use CautionI'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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto:freesurfer@nmr.mgh.harvard.edu; fsbuild fsbuild@contbay.com mailto:fsbuild@contbay.com; freesurfer-owner@nmr.mgh.harvard.edu mailto:freesurfer-owner@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use CautionDear 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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HI Mic, For pediatric data (not sure what age range you are processing), we use a different skullstripping tool. That might be useful for you. Let me know if this is stil of interest to you. Best, Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Michelangelo Fabbrizzi michefabb@gmail.com Sent: Saturday, August 5, 2023 11:33 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping
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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). [cid:6A95F4F6-43D6-4A47-AC66-0AA5655D152F]
[cid:2813DF67-351C-4FD8-BE04-583A06327C8B]
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
[cid:413358A2-4DA6-4B0A-BF45-0F4A38D6864B]
Il giorno 1 ago 2023, alle ore 00:22, Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@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 xxxx
Your help is greatly appreciated!
Michelangelo
Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu ha scritto:
External Email - Use Caution
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Michelangelo Fabbrizzi Sent: Sunday, July 30, 2023 9:32 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; fsbuild fsbuild@contbay.commailto:fsbuild@contbay.com; freesurfer-owner@nmr.mgh.harvard.edumailto:freesurfer-owner@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use Caution
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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Dear Lilla,
Thanks for your reply. Could you kindly point me to the skullstripping tool for pediatric data? Does it need InfantFS or works also with FS standard version?
Appreciated,
Mic
Il giorno 11 gen 2024, alle ore 18:02, Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu ha scritto:
HI Mic, For pediatric data (not sure what age range you are processing), we use a different skullstripping tool. That might be useful for you. Let me know if this is stil of interest to you. Best, Lilla From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Michelangelo Fabbrizzi <michefabb@gmail.com mailto:michefabb@gmail.com> Sent: Saturday, August 5, 2023 11:33 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use CautionDear 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). <Surfaces_without_shift_correction.png>
<Surfaces_with_shift_correction.png>
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
<Schermata 2023-08-05 alle 17.20.04.png>
Il giorno 1 ago 2023, alle ore 00:22, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> ha scritto:
External Email - Use Cautionthere 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 CautionDear 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 mailto:YHUANG43@mgh.harvard.edu ha scritto:
External Email - Use CautionI'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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto:freesurfer@nmr.mgh.harvard.edu; fsbuild fsbuild@contbay.com mailto:fsbuild@contbay.com; freesurfer-owner@nmr.mgh.harvard.edu mailto:freesurfer-owner@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use CautionDear 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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Douglas N. Greve -
Huang, Yujing -
Michelangelo Fabbrizzi -
Zollei, Lilla,Ph.D.