[Freesurfer] mri_watershed Error: read failed

[Schroder, Kirsten]

External Email - Use Caution

Dear Freesurfer developers,

I am currently conducting a research project in which I am running 7T MP2RAGE 
images in Freesurfer version 6.0.1 but have a run into an issue.

For 3 images I receive a watershed error stating “mri_watershed error: GLOBAL 
region of the brain empty!” which I tried to fix using the -skullstrip 
-no-wsgcaatlas flag but get different results: 1 image was successful but for 2 
images I get mri_watershed Error: read failed (see attachment). It appears that 
the last file created is the  001.mgz file hence there is no T1.mgz file 
created and Freesurfer therefore gives this error. I wanted to know if there is 
way to fix this as I have not been able to find a successful solution from the 
archive. I have also run the same dataset in Freesurfer version 7.2.0 and 
receive the same error for some scans.

Any help would be appreciated.

Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
uname -a: Linux pc8-009.ion.ucl.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Mar 
21 12:19:18 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux

Thank you,
Kirsten

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Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Michelangelo Fabbrizzi]

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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. 
>  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-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Michelangelo 
> Fabbrizzi mailto:michef...@gmail.com>>
> Sent: Saturday, August 5, 2023 11:33 AM
> To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping
>  
> External Email - Use Caution
> 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 
>>>>  <mailto:yhuan...@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-boun...@nmr.mgh.harvard.edu 
>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>>>>  
>>>> <mailto: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 
>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>; fsbuild  
>>>> <mailto:fsbu...@contbay.com>; freesurfer-ow...@nmr.mgh.

Re: [Freesurfer] mri_watershed Error while running recon-all

[Huang, Yujing]

External Email - Use Caution

I noticed all 292 images were processed in the same recon-all. I’m wondering if 
they are from the same subject.

If they are data from longitudinal study, you can process them with 
longitudinal pipeline -  
https://secure-web.cisco.com/1DWOFf8HXjewTlDOa5xZ86rZJrfN2Gj9YRwV79Y5tc02bjF1bZKUIUGPJilX4o2gwvaQE4gSTf22FcW8bxmoEK6tckr6lr47slov1v47TiBYt2OB7kLNsVYF8e1EJ-Rj0LhosG7bs9Lr7aGv5LH9-p9frssSGa5RxEKlUcJu7FGprWXkqNvin63GVMdjZOXNeg77kaSu0qCcLTvspy_wYthfv3y96BO1tb502D9KViGq0Kt373CLBKvESKZbo4HwpiKP1YotsAuashlkA2UdQkw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Iman Kianian
Sent: Saturday, August 26, 2023 9:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed Error while running recon-all


External Email - Use Caution
Hi there,
I was trying to extract the hippocampus parts of a T1 MRI dataset with 292 
samples as it is mentioned in the documentation ("MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1nDPXI5J4jwZAl4biV-62p60LDxcYoL5HoOu8ciGeukr-daTkNLAos6pzTU_ivS_hTeBcXxYb1nhNVynQ6WmxqtfWsNK2woqU2cqkmBHgX2QMV3qOBZsMD588H924UoZMonXno-pit9qdFJa-5KMTw-DtoJF_vtxDR0Cz0auoCKXb8-rGg_0bJlZlKw_vPFC7nXFedt6zPBEofAuwCEioT5w4K18k_eiqbWvH_bGHV5CrALrs5i1V2EvAXD0h5_ET6OPEOl8pjzcoCzcuzpj39Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala<https://secure-web.cisco.com/1BAyhN9FdUHAAqUD8DOQTWc8CqCVlTa3xgiGxxFItgCG2APPd1nEg4nE3AptgHfWColMe_ee-GG4i4us5pFR-e51GoSTb-V91YTdzNaKaTHiJURDzVAskrDzx4-OL41nRZUIXRxfqHTkxl3kOkQb2inZvcnrdhZWsuK6fu9M6-qXDo0PWGQXHRdlqYGBZkmVOJRcvcYSbe7LF4csk6Tjxpmj7Tl22CupnIdxYan7VkqsamjxZ9-3RYG6V2L0RDgMDPozCB--6uRxrY8gMdoT4jna17JZGlTlOnWIPASOwKZgtiBZQuemvhtgaduiq0rSSgjX8K3ik5Cg0NzHwpx_QxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala>").
 when I was trying to use the recon-all command, after almost 1 hour of 
processing I encountered this error:
"""
mri_watershed Error:
 GLOBAL region of the brain empty !
Command exited with non-zero status 1
"""

I appreciate your time for helping me. Note that I attached the recon-all.log 
for your review if it is needed.
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Re: [Freesurfer] mri_watershed Error while running recon-all

[Fischl, Bruce R.,PHD]

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This happens in one case or in all 292? You should follow the processing stream 
backwards to see where things first went wrong. It could be the skull 
stripping, but it might also be one of the inputs to it is already incorrect  
like the T1.mgz or transforms/talairach_with_skull.lta

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Iman Kianian
Sent: Saturday, August 26, 2023 9:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed Error while running recon-all


External Email - Use Caution
Hi there,
I was trying to extract the hippocampus parts of a T1 MRI dataset with 292 
samples as it is mentioned in the documentation ("MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1tcOiUdhh28Tixh--tJ08X0ReDV6gcct7x0LIeS8WLC4BHfFFMUY59drXYqBZ2cf1px1YLhKdeZpIOxujgkHwLWuNE4RzXCFCydRTjeN9DnUTC_aW-HtMD2nqifLEzFxZ1YbXPWAyRVLbKYdx-rKaH0d7ciRxJAPDXzKxVirvhpnEIXZOYsa0qr-8yjVBo6rUAwwuUxaR1h36IjYeySBCX6lJqOD_L08s9-UUJjxIB9yu62rydKM9sSroqe0d8VIs/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala<https://secure-web.cisco.com/1BAyhN9FdUHAAqUD8DOQTWc8CqCVlTa3xgiGxxFItgCG2APPd1nEg4nE3AptgHfWColMe_ee-GG4i4us5pFR-e51GoSTb-V91YTdzNaKaTHiJURDzVAskrDzx4-OL41nRZUIXRxfqHTkxl3kOkQb2inZvcnrdhZWsuK6fu9M6-qXDo0PWGQXHRdlqYGBZkmVOJRcvcYSbe7LF4csk6Tjxpmj7Tl22CupnIdxYan7VkqsamjxZ9-3RYG6V2L0RDgMDPozCB--6uRxrY8gMdoT4jna17JZGlTlOnWIPASOwKZgtiBZQuemvhtgaduiq0rSSgjX8K3ik5Cg0NzHwpx_QxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala>").
 when I was trying to use the recon-all command, after almost 1 hour of 
processing I encountered this error:
"""
mri_watershed Error:
 GLOBAL region of the brain empty !
Command exited with non-zero status 1
"""

I appreciate your time for helping me. Note that I attached the recon-all.log 
for your review if it is needed.
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Michelangelo Fabbrizzi]

External Email - Use Caution

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 
>>>>  <mailto:yhuan...@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-boun...@nmr.mgh.harvard.edu 
>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>>>>  
>>>> <mailto: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 
>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>; fsbuild  
>>>> <mailto:fsbu...@contbay.com>; freesurfer-ow...@nmr.mgh.harvard.edu 
>>>> <mailto:freesurfer-ow...@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 -sku

Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Douglas N. Greve]

   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:


   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-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

   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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Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Michelangelo Fabbrizzi]

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:
> 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-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
> 
>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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Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Huang, Yujing]

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-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

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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Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Huang, Yujing]

External Email - Use Caution

You don’t need ‘-careg’ if you just run autorecon3.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Michelangelo Fabbrizzi
Sent: Monday, July 31, 2023 8:55 AM
To: Freesurfer support list 
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 
mailto:yhuan...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 11:34 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; 
fsbuild mailto:fsbu...@contbay.com>>; 
freesurfer-ow...@nmr.mgh.harvard.edu<mailto:freesurfer-ow...@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 
mailto:michef...@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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Com

Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Michelangelo Fabbrizzi]

External Email - Use CautionDear Yujing,yes, I am using FS 7.3.2, so thanks I will try withrecon-all -s sub-01_recon -autorecon2 -caregshould 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  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-boun...@nmr.mgh.harvard.edu 
On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 11:34 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; freesurfer-ow...@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 <michef...@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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://www.massgeneralbrigham.org/complianceline  .___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Huang, Yujing]

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-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 11:34 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; 
freesurfer-ow...@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 
mailto:michef...@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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Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Michelangelo Fabbrizzi]

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 
>  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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[Freesurfer] mri_watershed and improvements of skullstripping

[Michelangelo Fabbrizzi]

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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[Freesurfer] mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter

[Camerino, I.L. (Ileana)]

External Email - Use Caution

Dear Freesurfer experts,



I am running recon all as part of the tractography pipeline on a group of 
stroke patients.

This is are the first lines of my log file:

/opt/freesurfer/6.0/bin/recon-all -s sub-056 -i 
/project/3015068.01/ilecam/Reolang/Data/sub-056/MP2RAGE_denoised_roi.nii.gz 
-all -sd /project/3015068.01/ilecam/Reolang/Freesurfer/ -qcache

subjid sub-056

setenv SUBJECTS_DIR /project/3015068.01/ilecam/Reolang/Freesurfer 
FREESURFER_HOME /opt/freesurfer/6.0

Actual FREESURFER_HOME /opt/freesurfer/6.0

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c



Recon all did not finished successfully because a watershed error:

Sorting...

mri_watershed Error:

Problem in the COG calculation:

T1.mgz may not contain properly normalized white-matter.

Confirm that T1.mgz has enough white-matter voxels of value 110.

If white-matter contains few if any voxels of value 110, try adding wm 
control-points to nu.mgz, and re-run recon-all.

I added many wm control-points to nu.mgz and to T1.mgz but when I re-run 
recon-all I still get the same error.

Please can you help me to solve this problem?

Thank you in advance
Best regards,
Ileana Camerino

PhD candidate
Donders Institute for Brain, Cognition and Behaviour

Centre for Cognition
Spinozabuilding
Room B02.25
Montessorilaan 3, 6525 HR Nijmegen
The Netherlands
Tel. +31-24 3612618




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Re: [Freesurfer] mri_watershed error: problem in the COG calcuation

[Julia Yang]

External Email - Use Caution

Hi Brunce,

The T1 files were too big that I couldn’t attach.
When I looked through the T1.mgz, the white matter intensity were only between 
70-90 in majority of the area.
Is there any way that I can adjust the intensity?

Kind Regards,

Julia

From: freesurfer-boun...@nmr.mgh.harvard.edu 

Date: Friday, 4 December 2020 at 4:54 am
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation
Make sure it looks reasonable (that there is a brain in there, and the 
intensities look ok). You can send it to us if you want

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 10:27 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation


External Email - Use Caution
Hi,

What will you be looking in the T1.mgz?
I am quite new to this field so have a very basic understanding of it.

Much appreciated.

Julia Yang


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Date: Thursday, 3 December 2020 at 12:39 pm
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation
Have you looked at the T1.mgz?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 8:37 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_watershed error: problem in the COG calcuation


External Email - Use Caution
Hi,

While running the recon_all, I bumped into this error message below.
\n mri_watershed -rusage 
/Users/Shared/PD-MCI/Freesurfer/PDMCI107/touch/rusage.mri_watershed.dat -T1 
-brain_atlas 
/Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca 
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n
Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for details
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*WATERSHED**
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.
Darwin med-cr-mtm0xv 18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 
PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64
recon-all -s PDMCI107 exited with ERRORS at Wed Nov


Recon_all failed without creating the brainmask.mgz.
I have attached files for possible solution.

  *   Recon-all.log
  *   Nu.mgz
  *   Talairach_with_skull.log
  *   Talairach.xfm

Any help would be much appreciated.

Kind Regards,

Julia Yang


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Re: [Freesurfer] mri_watershed error: problem in the COG calcuation

[Fischl, Bruce]

Make sure it looks reasonable (that there is a brain in there, and the 
intensities look ok). You can send it to us if you want

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 10:27 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation


External Email - Use Caution
Hi,

What will you be looking in the T1.mgz?
I am quite new to this field so have a very basic understanding of it.

Much appreciated.

Julia Yang


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Date: Thursday, 3 December 2020 at 12:39 pm
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation
Have you looked at the T1.mgz?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 8:37 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_watershed error: problem in the COG calcuation


External Email - Use Caution
Hi,

While running the recon_all, I bumped into this error message below.
\n mri_watershed -rusage 
/Users/Shared/PD-MCI/Freesurfer/PDMCI107/touch/rusage.mri_watershed.dat -T1 
-brain_atlas 
/Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca 
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n
Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for details
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*WATERSHED**
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.
Darwin med-cr-mtm0xv 18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 
PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64
recon-all -s PDMCI107 exited with ERRORS at Wed Nov


Recon_all failed without creating the brainmask.mgz.
I have attached files for possible solution.

  *   Recon-all.log
  *   Nu.mgz
  *   Talairach_with_skull.log
  *   Talairach.xfm

Any help would be much appreciated.

Kind Regards,

Julia Yang


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Re: [Freesurfer] mri_watershed error: problem in the COG calcuation

[Fischl, Bruce]

Have you looked at the T1.mgz?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 8:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed error: problem in the COG calcuation


External Email - Use Caution
Hi,

While running the recon_all, I bumped into this error message below.
\n mri_watershed -rusage 
/Users/Shared/PD-MCI/Freesurfer/PDMCI107/touch/rusage.mri_watershed.dat -T1 
-brain_atlas 
/Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca 
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n
Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for details
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*WATERSHED**
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.
Darwin med-cr-mtm0xv 18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 
PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64
recon-all -s PDMCI107 exited with ERRORS at Wed Nov


Recon_all failed without creating the brainmask.mgz.
I have attached files for possible solution.

  *   Recon-all.log
  *   Nu.mgz
  *   Talairach_with_skull.log
  *   Talairach.xfm

Any help would be much appreciated.

Kind Regards,

Julia Yang


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Re: [Freesurfer] mri_watershed

[Edoardo Pinzuti]

External Email - Use Caution

Is there a way to pass an already corrected brainmask file  or force the
function to do that so  all the subsequent  surf are created accordingly
without  using after mri_binarize?

On Fri, 5 Jun 2020, 7:52 p.m. Douglas N. Greve, 
wrote:

> mri_watershed creates brainmask.mgz, and the inner_skull should fit around
> that.
>
> On 6/3/2020 9:36 AM, Edoardo Pinzuti wrote:
>
> External Email - Use Caution
> Dear Freesurfer community,
>
> I have a question regarding the mri_watershed. Is the inner_skull
> extracted from the brain.mgz  which  gets masked by the
> brainmask.mgz automatically?
>
> Thanks
>
> ___
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>
>
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Re: [Freesurfer] mri_watershed

[Douglas N. Greve]

mri_watershed creates brainmask.mgz, and the inner_skull should fit 
around that.


On 6/3/2020 9:36 AM, Edoardo Pinzuti wrote:


External Email - Use Caution

Dear Freesurfer community,

I have a question regarding the mri_watershed. Is the inner_skull 
extracted from the brain.mgz  which  gets masked by the 
brainmask.mgz automatically?


Thanks

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[Freesurfer] mri_watershed

[Edoardo Pinzuti]

External Email - Use Caution

Dear Freesurfer community,

I have a question regarding the mri_watershed. Is the inner_skull extracted
from the brain.mgz  which  gets masked by the brainmask.mgz automatically?

Thanks
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Re: [Freesurfer] mri_watershed Error：Problem in the COG calculation

[Bruce Fischl]

Hi Abby

can you check the T1.mgz and see if it was normalized properly? Most of 
the WM should have an intensity around 110. If it doesn't, adding a couple 
of control points and rerunning may do the trick.


If you can't figure it out feel free to ftp us the tarred and gzipped 
subject dir.


cheers
Bruce


On Mon, 21 Jan 2019, Abby tang 
wrote:




External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to recon-all subjects but for some of my subjects I get the 
following error when I run recon-all comm
and:

 *WATERSHED**
Sorting...
mri_watershed Error: 
Problem in the COG calculation:

T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.

Linux abby-virtual-machine 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 
UTC 2018 x86_64 x86_64 x86_64 GNU/Lin
ux

recon-all -s 0078 exited with ERRORS at Sun Jan 20 20:16:12 CST 2019

I've searched the list and no similar errors have been reported. Does anyone 
have any thoughts on how to trouble-sho
ot this one? Also, Ive attached the recon-all.log in case it's of any use. 


Thank you!

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Re: [Freesurfer] mri_watershed Error

[Boris Rauchmann]

External Email - Use Caution

It would be great if you can have a look at the nu.mgz and talairach.xmf but 
unfortunately I´m not able to provide it in the mailing list.
Is there another way to send you the files?

Thanks, 
Boris

> Am 11.10.2018 um 22:04 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> the input to that watershed call is the T1.mgz, but it is already problematic 
> as you can see from the log. You should take a look at the nu.mgz and make 
> sure it is correct. You can also email me the nu.mgz and the talairach.xfm 
> (in the mri/transforms dir) if you want and I'll take a look
> cheers
> Bruce
> 
> 
> On Thu, 11 Oct 2018, Boris Rauchmann wrote:
> 
>>   External Email - Use Caution 
>> Hi again,
>> 
>> sorry. Please find attached the recon-all.log. I´m not sure how to check the 
>> input to watershed.
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Re: [Freesurfer] mri_watershed Error

[Bruce Fischl]

Hi Boris

the input to that watershed call is the T1.mgz, but it is already 
problematic as you can see from the log. You should take a look at the 
nu.mgz and make sure it is correct. You can also email me the nu.mgz and 
the talairach.xfm (in the mri/transforms dir) if you want and I'll take a 
look

cheers
Bruce


On Thu, 11 Oct 2018, Boris 
Rauchmann wrote:


   External Email - Use Caution 


Hi again,

sorry. Please find attached the recon-all.log. I´m not sure how to check the 
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Re: [Freesurfer] mri_watershed Error

[Boris Rauchmann]

External Email - Use Caution

Hi again,

sorry. Please find attached the recon-all.log. I´m not sure how to check the 
input to watershed.  

recon-all.log
Description: Binary data


Thanks,
Boris

> Am 11.10.2018 um 18:55 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> can you check to make sure that the input to the watershed looks ok? Also, in 
> general it is a lot easier for us to help if you send us the full command 
> line and screeen output and attach the recon-all.log
> 
> cheers
> Bruce
> 
> 
> On Thu, 11 Oct 2018, Boris Rauchmann wrote:
> 
>> External Email - Use Caution
>> When I run recon-all i get the follwing error message:
>>  mri_watershed Error: 
>>  GLOBAL region of the brain empty !
>> Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25
>> 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>> recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018
>> The .nii file looks fine. Can someone help me with this? 
>> Best,
>> Boris
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Re: [Freesurfer] mri_watershed Error

[Bruce Fischl]

Hi Boris

can you check to make sure that the input to the watershed looks ok? Also, 
in general it is a lot easier for us to help if you send us the full 
command line and screeen output and attach the recon-all.log


cheers
Bruce


On Thu, 11 Oct 
2018, Boris Rauchmann wrote:




External Email - Use Caution

When I run recon-all i get the follwing error message:

 mri_watershed Error: 
 GLOBAL region of the brain empty !
Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25
08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018

The .nii file looks fine. Can someone help me with this? 

Best,
Boris


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Re: [Freesurfer] mri_watershed Error

[Greve, Douglas N.,Ph.D.]

can you send the recon-all log file?

On 10/11/2018 11:22 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> When I run recon-all i get the follwing error message:
>
>  mri_watershed Error:
>  GLOBAL region of the brain empty !
> Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 
> 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018
>
> The .nii file looks fine. Can someone help me with this?
>
> Best,
> Boris
>
>
>
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[Freesurfer] mri_watershed Error

[Boris Rauchmann]

External Email - Use Caution

When I run recon-all i get the follwing error message:

 mri_watershed Error:
 GLOBAL region of the brain empty !
Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25
08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018

The .nii file looks fine. Can someone help me with this?

Best,
Boris
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Re: [Freesurfer] mri_watershed error/global region of the brain empty

[Bruce Fischl]

I think so. Or apply it with mri_convert -at
On Fri, 27 Apr 2018, miracle 
ozzoude wrote:




External Email - Use Caution

Hello Bruce, 
Thanks. Can I use tkregisterfv to visualize it?

Best, 
Paul


On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl  
wrote:
  Hi Paul

  that usually means something went wrong before the watershed. Check the 
input image to
  make sure that it and the talairach_with_skull.lta are ok

  cheers
  Bruce


  On Fri, 27 Apr 2018, miracle ozzoude wrote:


External Email - Use Caution

Hello FreeSurfer, 
While running recon-all on a subject, i got encountered an error 
during the
watershed step
(mri_watershed). How do i fix this problem? I have attached the
recon-all.log and
recon-all-status.log files. Thank you 

Best, 
Paul


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Re: [Freesurfer] mri_watershed error/global region of the brain empty

[miracle ozzoude]

External Email - Use Caution

Hello Bruce,

Thanks. Can I use tkregisterfv to visualize it?

Best,
Paul


On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl 
wrote:

> Hi Paul
>
> that usually means something went wrong before the watershed. Check the
> input image to make sure that it and the talairach_with_skull.lta are ok
>
> cheers
> Bruce
>
>
> On Fri, 27 Apr 2018, miracle ozzoude wrote:
>
>
>> External Email - Use Caution
>>
>>
>> Hello FreeSurfer,
>> While running recon-all on a subject, i got encountered an error during
>> the watershed step
>> (mri_watershed). How do i fix this problem? I have attached the
>> recon-all.log and
>> recon-all-status.log files. Thank you
>>
>> Best,
>> Paul
>>
>>
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> is
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Re: [Freesurfer] mri_watershed error/global region of the brain empty

[Bruce Fischl]

Hi Paul

that usually means something went wrong before the watershed. Check the 
input image to make sure that it and the talairach_with_skull.lta are ok


cheers
Bruce


On Fri, 27 Apr 2018, miracle 
ozzoude wrote:




External Email - Use Caution

Hello FreeSurfer, 
While running recon-all on a subject, i got encountered an error during the 
watershed step
(mri_watershed). How do i fix this problem? I have attached the recon-all.log 
and
recon-all-status.log files. Thank you 

Best, 
Paul

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[Freesurfer] mri_watershed error/global region of the brain empty

[miracle ozzoude]

External Email - Use Caution

Hello FreeSurfer,

While running recon-all on a subject, i got encountered an error during the
watershed step (mri_watershed). How do i fix this problem? I have attached
the recon-all.log and recon-all-status.log files. Thank you

Best,
Paul


recon-all.log
Description: Binary data


recon-all-status.log
Description: Binary data
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Re: [Freesurfer] mri_watershed Error: indices out of bounds

[Bruce Fischl]

Can you send us the recon-all.log?

> On Mar 30, 2018, at 11:32 AM, Darko Komnenić <komnen...@gmail.com> wrote:
> 
> Dear experts,
> while running recon-all on FreeSurfer 5.1.0 I encountered the following error:
> mri_watershed Error: indices out of bounds
> 
> I searched the email archive and found this thread:
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22=newest=1
> My problem seems identical to the one described by initial poster.
> The suggestion was to try the following command:
> set mdir=$SUBJECTS_DIR/$subject/mri
> mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz
> $mir/nu.mgz
> 
> When I tried it, the message I got was:
> mri_add_xform_to_header: could not open source file /nu.mgz
> No such file or directory
> And indeed such file  does not exist in the mri subfolder of my
> current subject's folder.
> 
> Any further suggestions on how to fix this?  Like the person asking
> originally, this is the only participant where it happened, for
> others, recon-all finished without error and all the images were
> acquired in the same scanner.
> Thanks in advance!
> Best,
> Darko
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> 


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[Freesurfer] mri_watershed Error: indices out of bounds

[Darko Komnenić]

Dear experts,
while running recon-all on FreeSurfer 5.1.0 I encountered the following error:
mri_watershed Error: indices out of bounds

I searched the email archive and found this thread:
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22=newest=1
My problem seems identical to the one described by initial poster.
The suggestion was to try the following command:
set mdir=$SUBJECTS_DIR/$subject/mri
mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz
$mir/nu.mgz

When I tried it, the message I got was:
mri_add_xform_to_header: could not open source file /nu.mgz
No such file or directory
And indeed such file  does not exist in the mri subfolder of my
current subject's folder.

Any further suggestions on how to fix this?  Like the person asking
originally, this is the only participant where it happened, for
others, recon-all finished without error and all the images were
acquired in the same scanner.
Thanks in advance!
Best,
Darko
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[Freesurfer] mri_watershed help

[Kanoff, Kristen Elise]

Dear Freesurfer community,

I am using the mri_watershed command to create BEM surfaces and have run into 
an issue with a large posterior chunk of skull being treated as brain.

[cid:image002.jpg@01D2D47E.75797E70]

I have attempted the following to correct the issue:


1.Removed the -atlas flag

2.   Used -less to decrease the transition threshold used during the fine 
surface deformation

3.   Used -man to set more/less stringent parameters for the intensity 
values

4.   Adjusted the preflooding height

5.   Used the -first_temp flag in combination with -man

Removing the -atlas flag and using -less to shrink the surface seemed to 
provide the best result (image shown above) but the issue is not entirely 
resolved.  Does anyone have any suggestions for a better approach?  I can 
manually adjust the brain mask created during the recon-all process but there 
doesn't seem to be a way to do something similar when using mri_watershed alone.

I also attempted to use the -wat+temp flag (command:  mri_watershed -wat+temp 
-useSRAS -surf ./surfout ./T1.mgz ./brainvol) but I am getting the following 
error:

mri_watershed Error:
 Problem in find normal

The full command window output is attached.

Any help/suggestions would be very much appreciated!

Best,

Kristen


osboxes@osboxes:~/Documents/freesurfer/subjects/iDBS007/mri$ mri_watershed 
-wat+temp -useSRAS -surf ./surfout ./T1.mgz ./brainvol

Mode:  watershed algorithm + first template smoothing
Mode:  use surfaceRAS to save surface vertex positions
Mode:  Saving out BEM surfaces

*
The input file is ./T1.mgz
The output file is ./brainvol

*WATERSHED**
Sorting...
  T1-weighted MRI image
  modification of the preflooding height to 15 percent
  Count how many 110 voxels are present :  139360

  Find the largest 110-component...
 heap usage = 200464 Kbytes.
 current max segment has 111799 voxels
 removing small segments (less than 1 percent of maxarea).
 heap usage = 131784 Kbytes.
 removing small segments (less than 1 percent of maxarea).done
  And identify it as the main brain basin...done
  Main component: 111799 voxels
  first estimation of the COG coord: x=130 y=126 z=113 r=77
  first estimation of the main basin volume: 1973574 voxels
  global maximum in x=112, y=110, z=78, Imax=255
  CSF=24, WM_intensity=110, WM_VARIANCE=5
  WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
  preflooding height equal to 15 percent
done.
Analyze...

  main basin size= 1212297 voxels, voxel volume =1.000 
 = 1212297 mmm3 = 1212.297 cm3
done.
PostAnalyze...
  ambiguous basin, merged: at least 6 ambiguous voxels; size: 213 voxels
  ambiguous basin, merged: at least 6 ambiguous voxels; size: 167 voxels
  ambiguous basin, merged: at least 17 ambiguous voxels; size: 4603 voxels
  ambiguous basin, merged: at least 12 ambiguous voxels; size: 1336 voxels
  ambiguous basin, merged: at least 6 ambiguous voxels; size: 203 voxels
  ambiguous basin, merged: at least 50 ambiguous voxels; size: 117655 voxels
  * 6 basin(s) merged in 4 iteration(s)
  * 124177 voxel(s) added to the main basin
  ambiguous basin, non merged: 8 ambiguous voxels; size: 2743 voxels
done.

TEMPLATE DEFORMATION

  second estimation of the COG coord: x=129,y=126, z=107, r=10065 iterations
  mri_strip_skull: done peeling brain

Brain Size = 1470715 voxels, voxel volume = 1.000 mm3
   = 1470715 mmm3 = 1470.715 cm3

  outer skin surface matching...
mri_watershed Error: 
 Problem in find normal 
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[Freesurfer] mri_watershed script not working

[Mario Rossi]

Hello FreeSurfer Developers and experts,

I am trying to run our FSPGR sequences using the  -mri_watershed script, but I 
am not able to set and vary the -t threshold.
The aim of my work is to calculate the BPF in order to quantify parenchymal 
atrophy in patients with Multiple Sclerosis.

Instead of using the whole "-recon-all" command, I have tried to reduce the 
amount of datas (and the very long  time needed to calculate them) performing 
this script:

"-mri_watershed -atlas"

The result of the extraction of the brain is good and fast, but I still could 
need to adjust the cut limits. I have tried to modify it into this new script:

"-mri_watershed -atlas -t X"

(where "X" stands for a variable between 0 and 50) but in this case, no matter 
what "X" I choose the results are all identical.

Is it possible to set a -t threshold using -atlas?
If not, can you suggest us how to change our approach?
Is it possibile to use freesurfer with FLAIR sequences with the same aim 
(extract the BPF to evaluate  brain atrophy)?

Best regards,
Mario Rossi


1) FreeSurfer version:  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform: Linux Mint  1 Debian MATE 64-bit



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Re: [Freesurfer] mri_watershed seed point

[Antonin Skoch]

Dear Kristen,

looking at the source code of mri_watershed, the seed point has to be specified 
in the format:
-s i j k

and the option can be specified more than once when you want to add more seed 
points (30 seed points is maximum).

i.e., when you want to input seed points in coordinates 50,60,70, and 
80,90,100, the option would be:
-s 50 60 70 -s 80 90 100

Regards,

Antonin Skoch



Hello FreeSurfer Community,

I am attempting to use mri_watershed to create BEM surfaces, but for some of my 
subjects part of the cerebellum is being cut off.  Adjusting the threshold was 
not sufficient, so I attempted to add a seed point in the cerebellum using the 
following command:mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81] 
./T1.mgz 
./brainvol

The coordinates for the seed point are from the T1.mgz image.  I reran 
mri_watershed and the seed point does not seem to be taken into consideration 
so I'm thinking that the input format I used may be wrong.  Could someone 
please tell me if I am not using the proper input format?  And what format to 
use if I wish to add multiple seed points?  Command output is attached.

Thanks in advance!

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[Freesurfer] mri_watershed seed point

[Kanoff, Kristen Elise]

Hello FreeSurfer Community,

I am attempting to use mri_watershed to create BEM surfaces, but for some of my 
subjects part of the cerebellum is being cut off.  Adjusting the threshold was 
not sufficient, so I attempted to add a seed point in the cerebellum using the 
following command:

mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81] ./T1.mgz 
./brainvol

The coordinates for the seed point are from the T1.mgz image.  I reran 
mri_watershed and the seed point does not seem to be taken into consideration 
so I'm thinking that the input format I used may be wrong.  Could someone 
please tell me if I am not using the proper input format?  And what format to 
use if I wish to add multiple seed points?  Command output is attached.

Thanks in advance!

Kristen


Kristen Kanoff
Clinical Research Coordinator II
Department of Neurology
Massachusetts General Hospital
Boston, MA
Ph: 617-726-3958
osboxes@osboxes:~/Documents/freesurfer/subjects/iDBS002/mri$ mri_watershed 
-atlas -useSRAS -surf ./surfout -s [105 182 81] ./T1.mgz ./brainvol

Mode:  Atlas analysis
Mode:  use surfaceRAS to save surface vertex positions
Mode:  Saving out BEM surfaces

*
The input file is ./T1.mgz
The output file is ./brainvol

*WATERSHED**
Sorting...
  T1-weighted MRI image
  modification of the preflooding height to 15 percent
  Count how many 110 voxels are present :  176432

  Find the largest 110-component...
 heap usage = 336340 Kbytes.
 current max segment has 154566 voxels
 removing small segments (less than 1 percent of maxarea).
 heap usage = 130864 Kbytes.
 removing small segments (less than 1 percent of maxarea).done
  And identify it as the main brain basin...done
  Main component: 154566 voxels
  first estimation of the COG coord: x=128 y=122 z=94 r=81
  first estimation of the main basin volume: 2241917 voxels
  global maximum in x=146, y=114, z=55, Imax=255
  CSF=24, WM_intensity=110, WM_VARIANCE=5
  WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
  preflooding height equal to 15 percent
done.
Analyze...

  main basin size=34171332 voxels, voxel volume =1.000 
 = 34171332 mmm3 = 34171.332 cm3
done.
PostAnalyze...
  ambiguous basin, merged: at least 12 ambiguous voxels; size: 1490 voxels
  ambiguous basin, merged: at least 4 ambiguous voxels; size: 60 voxels
  ambiguous basin, merged: at least 11 ambiguous voxels; size: 1280 voxels
  ambiguous basin, merged: at least 7 ambiguous voxels; size: 260 voxels
  ambiguous basin, merged: at least 10 ambiguous voxels; size: 913 voxels
  ambiguous basin, merged: at least 7 ambiguous voxels; size: 307 voxels
  * 6 basin(s) merged in 4 iteration(s)
  * 4310 voxel(s) added to the main basin
  ambiguous basin, non merged: 6 ambiguous voxels; size: 2335 voxels
done.

TEMPLATE DEFORMATION

  second estimation of the COG coord: x=128,y=120, z=92, r=12891 iterations
 couldn't find WM with original limits - expanding ^^

   GLOBAL  CSF_MIN=1, CSF_intensity=2, CSF_MAX=31 , nb = 43064
 Problem with the least square interpolation in GM_MIN calculation.
   
 CSF_MAX  TRANSITION  GM_MIN  GM
GLOBAL 
  before analyzing :31,  29,28,   54
  after  analyzing :20,  29,29,   35
  mri_strip_skull: done peeling brain
  highly tesselated surface with 10242 vertices
  matching...59 iterations

*VALIDATION*
curvature mean = -0.013, std = 0.011
curvature mean = 67.196, std = 9.490

Rigid alignment...
  scanning 32.00 degree nbhd, min sse =  6.39 at ( 0.00,  8.00,  8.00)
  scanning 16.00 degree nbhd, min sse =  6.10 at ( 0.00, -4.00, -4.00)
  scanning  8.00 degree nbhd, min sse =  6.10 at ( 0.00,  0.00,  0.00)
  scanning  4.00 degree nbhd, min sse =  6.08 at ( 1.00,  1.00,  1.00)
done
  before rotation: sse = 6.68, sigma = 13.72
  after  rotation: sse = 6.08, sigma = 10.80
Localization of inacurate regions: Erosion-Dilation steps
  the sse mean is  7.43, its var is 10.75   
  before Erosion-Dilatation  6.23% of inacurate vertices
  after  Erosion-Dilatation  9.18% of inacurate vertices
  Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

FINAL ITERATIVE TEMPLATE DEFORMATION
Compute Local values csf/gray
Fine Segmentation...40 iterations

  mri_strip_skull: done peeling brain

Brain Size = 1413043 voxels, voxel volume = 1.000 mm3
   = 1413043 mmm3 = 1413.043 cm3

  outer skin surface matching...187 iterations

**
Saving ./brainvol
done
mri_watershed utimesec513.928000
mri_watershed 

[Freesurfer] mri_watershed for infants or NHP

[Mahmoud]

Dear experts,

I'm trying to adopt the HCP pipeline to our own data but at it is
originally developed for human adults it fails frequently on my data. A big
chunk of the pipeline is based on FreeSurfer so I thought it should be most
relevant to ask my question here.

the main problem I have here is that mri_watershed fails so the rest of the
pipeline cannot proceed. The errors are usually like below:

TEMPLATE DEFORMATION

  second estimation of the COG coord: x=128,y=131, z=124, r=39161
iterations
 couldn't find WM with original limits - expanding ^^

   GLOBAL  CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 38180
  RIGHT_CERCSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1043712479
  LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1117744481
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1064196139
 LEFT_BRAINCSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1050954328
OTHER  CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1062732290
mri_watershed Error:
 GLOBAL region of the brain empty !
##

or

*WATERSHED**
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.
#

I really appreciate any help or direction.

Thank you!
Mahmoud
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Re: [Freesurfer] mri_watershed mask and skull surfaces

[Bruce Fischl]

Hi Sam

if you want us to help you, you need to provide us with the full 
command line and screen output (at least!)


cheers
Bruce
On Tue, 21 Jul 2015, Sam Zorowitz 
wrote:



Hi all,
I am using mri_watershed to create skull surfaces for a cohort of subjects
for whom we were unable to collect a FLASH sequence. To improve the
estimation of the inner skull layer, I would like to use edited brainmasks.
However whenever I supply the -mask flag, and only when I supply -mask flag
to mri_watershed, the code does not run; it only brings up the help screen. 

So two questions:
(1) Is the -mask flag in mri_watershed doing what I think it is doing? Is it
masking the T1 image to only the brain so that the inner skull layer will be
estimated from the brainmask?
(2) Am I using the -mask flag correctly? I get the same result if I use
mri_watershed -mask and mri_watershed -mask path to mask. Should I be
doing something differently?

All the best,
Sam

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[Freesurfer] mri_watershed mask and skull surfaces

[Sam Zorowitz]

Hi all,

I am using mri_watershed to create skull surfaces for a cohort of subjects
for whom we were unable to collect a FLASH sequence. To improve the
estimation of the inner skull layer, I would like to use edited brainmasks.
However whenever I supply the -mask flag, and only when I supply -mask flag
to mri_watershed, the code does not run; it only brings up the help screen.

So two questions:
(1) Is the -mask flag in mri_watershed doing what I think it is doing? Is
it masking the T1 image to only the brain so that the inner skull layer
will be estimated from the brainmask?
(2) Am I using the -mask flag correctly? I get the same result if I use
mri_watershed -mask and mri_watershed -mask path to mask. Should I be
doing something differently?

All the best,
Sam
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Re: [Freesurfer] mri_watershed Error: indices out of bounds

[Ani Varjabedian]

Hello Edgar,

We think we were able to isolate the problem. Version 5.1 is failing to 
apply the talairach transform to the nu.mgz. It gets computed and 
applied to the orig.mgz but then not transferred during the next step.


When mri_normalize tries to run without this information, it fails, and 
then this leads to watershed failing as well. mri_normalize usually 
tries to fallback on other options if the talairach transform isn't 
present, and this can work most of the time, but in some cases it fails 
(which can explain why this subject in particular fails but other 
subjects go through just fine).


try:

set mdir=$SUBJECTS_DIR/$subject/mri
mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz 
$mir/nu.mgz


to add the transform to your nu.mgz header. Then if you run recon-all 
from this step onwards (you could even use recon-all -make all), it 
should work.



Let me know if you try this, and if you have some success.

Thank you,
Ani Varjabedian

On 04/02/2015 04:26 PM, Ani Varjabedian wrote:

Hello Edgar,

I am going to be looking at your case and seeing if I can replicate 
the error. I have your .nii file and will run it through our 
processing stream here, but could you send me your subject folder so 
that I can look through your files/logs to give me some more information?


You can upload the subject folder through filedrop2.0 which is a bit 
easier to use, as long as your folder is under 2GB!

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thank you,
Ani Varjabedian

On 04/02/2015 11:23 AM, Edgar Busovaca wrote:

Hello Bruce,

I just wanted to touch base regarding the Indices_oob.nii subject I 
had sent to MGH.  Were you by any chance able to detect the issue 
with running recon-all on this subject.  Thanks in advance for taking 
a look at this.


Best regards,
Edgar Busovaca


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Re: [Freesurfer] mri_watershed Error: indices out of bounds

[Ani Varjabedian]

Hello Edgar,

I am going to be looking at your case and seeing if I can replicate the 
error. I have your .nii file and will run it through our processing 
stream here, but could you send me your subject folder so that I can 
look through your files/logs to give me some more information?


You can upload the subject folder through filedrop2.0 which is a bit 
easier to use, as long as your folder is under 2GB!

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thank you,
Ani Varjabedian

On 04/02/2015 11:23 AM, Edgar Busovaca wrote:

Hello Bruce,

I just wanted to touch base regarding the Indices_oob.nii subject I 
had sent to MGH.  Were you by any chance able to detect the issue with 
running recon-all on this subject.  Thanks in advance for taking a 
look at this.


Best regards,
Edgar Busovaca


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Re: [Freesurfer] mri_watershed Error: indices out of bounds

[Edgar Busovaca]

Hello Bruce,

I just wanted to touch base regarding the Indices_oob.nii subject I had
sent to MGH.  Were you by any chance able to detect the issue with running
recon-all on this subject.  Thanks in advance for taking a look at this.

Best regards,
Edgar Busovaca
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Re: [Freesurfer] mri_watershed Error: indices out of bounds

[Ani Varjabedian]

Hello Edgar,

Could you upload the whole subject folder? I could try to run it through 
recon all here and see if I can reproduce the error. It would also allow 
me to look through your log files to see if I can spot anything that 
could be causing this issue.


You can use FileDrop2.0 if the directory is under 2GB
https://gate.nmr.mgh.harvard.edu/filedrop2/

Thank you,
Ani Varjabedian

On 03/25/2015 11:06 AM, Edgar Busovaca wrote:

Hello Bruce,

I took a look at the file with freeview and I can't identify anything 
peculiar about the data.  The file is named Indices_oob.nii and has 
been uploaded to /transfer/incoming on the FTP file exchange server.  
Thank you for your swift reply and in advance for your time.


Best regards,
Edgar Busovaca

On Tue, Mar 24, 2015 at 5:34 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote:


Hi Edgar

the LINE SEARCH thing is not a real problem. I've never seen
indices out of bounds before though. Is there anything strange
about your dataset? Does freeview display it properly (that is,
are what freeview thinks the RAS dirs the correct anatomical
ones)? If you upload the dataset we'll see if we can replicate and
fix the problem

cheers
Bruce

 On Tue, 24 Mar 2015, Edgar Busovaca wrote:

Dear Freesurfer users,
I have attempted to process a subject (.nii type input)
through recon-all
-all, but for some reason the processing gambit is terminated
early ( during
the skullstrip).

During skullstripping the following warning appears twice:

IFLAG= -1  LINE SEARCH FAILED.  SEE DOCUMENTATION OF ROUTINE
MCSRCH ERROR
RETURN OF LINE SEARCH:  INFO=3 POSSIBLE CAUSES FUNCTION OR
GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof WuasiNewtonEMA: 007:
-log(p) =
10341.8 tol 0.10

following the skullstrip step in ***WATERSHED
the following
appears:

mri_watershed Error: indices out of bounds


Oddly, this particular subject failed where the rest of the
data set
successfully completed recon-all -all.



As a reference I am running freesurfer 5.1
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
RedHat release: CentOS release 6.5 (Final)
Kernel info: Linux 2.6.32-431.11.2.e16.x86_64 x86_64


Is there a flag to push this subject through recon-all?

Thanks in advance for your time.

Best,
Edgar Busovaca


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Re: [Freesurfer] mri_watershed Error: indices out of bounds

[Edgar Busovaca]

Hello Bruce,

I took a look at the file with freeview and I can't identify anything
peculiar about the data.  The file is named Indices_oob.nii and has been
uploaded to /transfer/incoming on the FTP file exchange server.  Thank you
for your swift reply and in advance for your time.

Best regards,
Edgar Busovaca

On Tue, Mar 24, 2015 at 5:34 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 Hi Edgar

 the LINE SEARCH thing is not a real problem. I've never seen indices out
 of bounds before though. Is there anything strange about your dataset?
 Does freeview display it properly (that is, are what freeview thinks the
 RAS dirs the correct anatomical ones)? If you upload the dataset we'll see
 if we can replicate and fix the problem

 cheers
 Bruce

  On Tue, 24 Mar 2015, Edgar Busovaca wrote:

  Dear Freesurfer users,
 I have attempted to process a subject (.nii type input) through recon-all
 -all, but for some reason the processing gambit is terminated early (
 during
 the skullstrip).

 During skullstripping the following warning appears twice:

 IFLAG= -1  LINE SEARCH FAILED.  SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
 RETURN OF LINE SEARCH:  INFO=3 POSSIBLE CAUSES FUNCTION OR GRADIENT ARE
 INCORRECT OR INCORRECT TOLERANCESoutof WuasiNewtonEMA: 007: -log(p) =
 10341.8 tol 0.10

 following the skullstrip step in ***WATERSHED the
 following
 appears:

 mri_watershed Error: indices out of bounds


 Oddly, this particular subject failed where the rest of the data set
 successfully completed recon-all -all.



 As a reference I am running freesurfer 5.1
 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
 RedHat release: CentOS release 6.5 (Final)
 Kernel info: Linux 2.6.32-431.11.2.e16.x86_64 x86_64


 Is there a flag to push this subject through recon-all?

 Thanks in advance for your time.

 Best,
 Edgar Busovaca


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 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
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 error
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Re: [Freesurfer] mri_watershed Error: indices out of bounds

[Bruce Fischl]

Hi Edgar

the LINE SEARCH thing is not a real problem. I've never seen indices out 
of bounds before though. Is there anything strange about your dataset? 
Does freeview display it properly (that is, are what freeview thinks the 
RAS dirs the correct anatomical ones)? If you upload the dataset we'll see 
if we can replicate and fix the problem


cheers
Bruce
 On Tue, 24 Mar 2015, Edgar Busovaca 
wrote:



Dear Freesurfer users,
I have attempted to process a subject (.nii type input) through recon-all
-all, but for some reason the processing gambit is terminated early ( during
the skullstrip).

During skullstripping the following warning appears twice:

IFLAG= -1  LINE SEARCH FAILED.  SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH:  INFO=3 POSSIBLE CAUSES FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof WuasiNewtonEMA: 007: -log(p) =
10341.8 tol 0.10

following the skullstrip step in ***WATERSHED the following
appears:

mri_watershed Error: indices out of bounds


Oddly, this particular subject failed where the rest of the data set
successfully completed recon-all -all.



As a reference I am running freesurfer 5.1
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
RedHat release: CentOS release 6.5 (Final)
Kernel info: Linux 2.6.32-431.11.2.e16.x86_64 x86_64


Is there a flag to push this subject through recon-all?

Thanks in advance for your time.

Best,
Edgar Busovaca

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[Freesurfer] mri_watershed Error: indices out of bounds

[Edgar Busovaca]

Dear Freesurfer users,

I have attempted to process a subject (.nii type input) through recon-all
-all, but for some reason the processing gambit is terminated early (
during the skullstrip).

During skullstripping the following warning appears twice:

IFLAG= -1  LINE
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[Freesurfer] mri_watershed Error: indices out of bounds

[Edgar Busovaca]

Dear Freesurfer users,

I have attempted to process a subject (.nii type input) through recon-all
-all, but for some reason the processing gambit is terminated early (
during the skullstrip).

During skullstripping the following warning appears twice:

IFLAG= -1  LINE SEARCH FAILED.  SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH:  INFO=3 POSSIBLE CAUSES FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof WuasiNewtonEMA: 007: -log(p) =
10341.8 tol 0.10

following the skullstrip step in ***WATERSHED the following
appears:

mri_watershed Error: indices out of bounds


Oddly, this particular subject failed where the rest of the data set
successfully completed recon-all -all.



As a reference I am running freesurfer 5.1
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
RedHat release: CentOS release 6.5 (Final)
Kernel info: Linux 2.6.32-431.11.2.e16.x86_64 x86_64


Is there a flag to push this subject through recon-all?

Thanks in advance for your time.

Best,
Edgar Busovaca
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[Freesurfer] mri_watershed -brain_atlas undocumented?

[tvg[fs]]

- This is a repost. It seems it did not come trough yesterday.
Apologies if this becomes a double post -



Hi all,

I noticed that during skull stripping the standard recon-all pipeline
uses option -brain_atlas in the routine mri_watershed. However
documentation of this argument cannot be found in the help section or
on the website.

mri_watershed --help | less -p atlas
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas)

Is this an undocumented flag or simply a synonym for -atlas? Does
the -brain_atlas flag take an extra argument to specify the atlas?

Thanks,
Tom

Specs:
Mac OS X 10.8.5
freesurfer-Darwin-lion-stable-pub-v5.3.0
$ mri_watershed --version
stable5
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Re: [Freesurfer] mri_watershed -brain_atlas undocumented?

[Bruce Fischl]

Hi Tom

I'll cc Flo who wrote this code (a long time ago!). I think the 
-brain_atlas flag takes a gca atlas and uses it to avoid large-scale 
errors, while -atlas uses some built-in statistics about the shape and size 
of e.g. the cerebellum to avoid erasing it accidentally. Flo can correct me 
if I'm wrong :)

cheers
Bruce



On Tue, 4 Nov 2014, tvg[fs] wrote:

 - This is a repost. It seems it did not come trough yesterday.
 Apologies if this becomes a double post -



 Hi all,

 I noticed that during skull stripping the standard recon-all pipeline
 uses option -brain_atlas in the routine mri_watershed. However
 documentation of this argument cannot be found in the help section or
 on the website.

 mri_watershed --help | less -p atlas
 https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas)

 Is this an undocumented flag or simply a synonym for -atlas? Does
 the -brain_atlas flag take an extra argument to specify the atlas?

 Thanks,
 Tom

 Specs:
 Mac OS X 10.8.5
 freesurfer-Darwin-lion-stable-pub-v5.3.0
 $ mri_watershed --version
 stable5
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[Freesurfer] mri_watershed -brain_atlas undocumented?

[tvg[fs]]

Hi all,

I noticed that during skull stripping the standard recon-all pipeline
uses option -brain_atlas in the routine mri_watershed. However
documentation of this argument cannot be found in the help section or
on the website.

mri_watershed --help | less -p atlas
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas)

Is this an undocumented flag or simply a synonym for -atlas. Does
the -brain_atlas flag take an extra argument to specify the atlas?

Thanks,
Tom

Specs:
Mac OS X 10.8.5
freesurfer-Darwin-lion-stable-pub-v5.3.0
 mri_watershed --version
stable5
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[Freesurfer] mri_watershed problems

[Sam Zorowitz]

Dear Freesurfer community,

I am running into issues with mri_watershed, which I am using the create
the BEM surfaces. In testing different preflooding height threshold
(recommended for accurate skull-stripping), I am running into the issues
that an -h 56 produces results where the cerebellum is stripped away, but
-h 57 leaves far too much non-brain material in the image. As a result, my
BEM surfaces are unrepresentative of the brain (either shrunken in or
enlarged).

I do, however, already have a satisfying brain-mask. Is there a way to pass
the brain mask to mri_watershed to create new BEM surfaces without it
creating a new brain mask?

Sam Zorowitz

Clinical Research Coordinator
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
Massachusetts General Hospital
149 13th Street, Rm 2620e
Charlestown, MA 02129
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Re: [Freesurfer] mri_watershed: really bad skull stripping

[Úrsula Pérez Ramírez]

Hi all,
Thanks Bruce for your recommendation, with recon-all I obtain a much better 
skull stripping. Now I'm going to change thresholds because at the top and 
bottom slices the segmentation is inadequate: central segmentation is missing. 
Cheers,
Úrsula

Date: Fri, 29 Aug 2014 11:48:51 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping

you can give any format we support to recon-all as the input, including 
.mgz
 
cheers
Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
 
 Hi Bruce,
 
 thank you very much for your fast answer. I'm running outside recon-all,
 only with mri_watershed. Thanks, that could help. Which are the options for
 recon-all if I have already the .mgz file?, I'm getting errors, appart from
 the warning for updating tcsh.
 
 Cheers,
 Ursula
 
 Date: Fri, 29 Aug 2014 11:23:06 -0400
 From: fis...@nmr.mgh.harvard.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
 
 Hi Arsula
 
 are you running this through recon-all or outside of it? The skull 
 stripping works better after the intensity normalization  that is part of 
 recon-all
 
 cheers
 Bruce

 
 On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
 
  
  Hello,
  
  
  I’m new with FreeSurfer and I’m getting a really bad skull stripping (almo
 st
  nothing) with mri_watershed –atlas in images converted from DICOM to .mgz
  with mri_convert. I lowered the threshold but did not improved considerabl
 y.
  I have tried with a subject from the tutorial dataset and it’s OK. What ca
 n
  be the problem?
  
  Thank you very much!
  
  
  Úrsula
  
  
 
 
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 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
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Re: [Freesurfer] mri_watershed: really bad skull stripping

[Bruce Fischl]

I'm glad to hear it improved.

cheers
Bruce


On Sat, 30 Aug 2014, Úrsula Pérez Ramírez wrote:


Hi all,
Thanks Bruce for your recommendation, with recon-all I obtain a much better
skull stripping. Now I'm going to change thresholds because at the top and
bottom slices the segmentation is inadequate: central segmentation is
missing. 

Cheers,

Úrsula

Date: Fri, 29 Aug 2014 11:48:51 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping

you can give any format we support to recon-all as the input, including 
.mgz


cheers
Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:

 Hi Bruce,
 
 thank you very much for your fast answer. I'm running outside recon-all,

 only with mri_watershed. Thanks, that could help. Which are the options fo
r
 recon-all if I have already the .mgz file?, I'm getting errors, appart fro
m
 the warning for updating tcsh.
 
 Cheers,

 Ursula
 
 Date: Fri, 29 Aug 2014 11:23:06 -0400

 From: fis...@nmr.mgh.harvard.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
 
 Hi Arsula
 
 are you running this through recon-all or outside of it? The skull 
 stripping works better after the intensity normalization  that is part of 
 recon-all
 
 cheers

 Bruce

 
 On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
 
  
  Hello,
  
  
  I’m new with FreeSurfer and I’m getting a really bad skull stripping (al

mo
 st
  nothing) with mri_watershed –atlas in images converted from DICOM to .mg
z
  with mri_convert. I lowered the threshold but did not improved considera
bl
 y.
  I have tried with a subject from the tutorial dataset and it’s OK. What 
ca

 n
  be the problem?
  
  Thank you very much!
  
  
  Úrsula
  
  
 
 
 ___ Freesurfer mailing list

 Freesurfer@nmr.mgh.harvard.edu
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on
 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
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[Freesurfer] mri_watershed: really bad skull stripping

[Úrsula Pérez Ramírez]

Hello,


I’m new with
FreeSurfer and I’m getting a really bad skull stripping (almost nothing) with 
mri_watershed
–atlas in images converted from DICOM to .mgz with mri_convert. I lowered the 
threshold but did not improved considerably. I have tried
with a subject from the tutorial dataset and it’s OK. What can be the problem?

Thank you very much!


Úrsula

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Re: [Freesurfer] mri_watershed: really bad skull stripping

[Bruce Fischl]

Hi Arsula

are you running this through recon-all or outside of it? The skull 
stripping works better after the intensity normalization  that is part of 
recon-all


cheers
Bruce


On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:



Hello,


I’m new with FreeSurfer and I’m getting a really bad skull stripping (almost
nothing) with mri_watershed –atlas in images converted from DICOM to .mgz
with mri_convert. I lowered the threshold but did not improved considerably.
I have tried with a subject from the tutorial dataset and it’s OK. What can
be the problem?

Thank you very much!


Úrsula


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Re: [Freesurfer] mri_watershed: really bad skull stripping

[Úrsula Pérez Ramírez]

Hi Bruce,

thank you very much for your fast answer. I'm running outside recon-all, only 
with mri_watershed. Thanks, that could help. Which are the options for 
recon-all if I have already the .mgz file?, I'm getting errors, appart from the 
warning for updating tcsh.

Cheers,
Ursula

Date: Fri, 29 Aug 2014 11:23:06 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping

Hi Arsula
 
are you running this through recon-all or outside of it? The skull 
stripping works better after the intensity normalization  that is part of 
recon-all
 
cheers
Bruce
 
 
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
 
 
 Hello,
 
 
 I’m new with FreeSurfer and I’m getting a really bad skull stripping (almost
 nothing) with mri_watershed –atlas in images converted from DICOM to .mgz
 with mri_convert. I lowered the threshold but did not improved considerably.
 I have tried with a subject from the tutorial dataset and it’s OK. What can
 be the problem?
 
 Thank you very much!
 
 
 Úrsula
 
 


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Re: [Freesurfer] mri_watershed: really bad skull stripping

[Bruce Fischl]

you can give any format we support to recon-all as the input, including 
.mgz


cheers
Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:


Hi Bruce,

thank you very much for your fast answer. I'm running outside recon-all,
only with mri_watershed. Thanks, that could help. Which are the options for
recon-all if I have already the .mgz file?, I'm getting errors, appart from
the warning for updating tcsh.

Cheers,
Ursula

Date: Fri, 29 Aug 2014 11:23:06 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping

Hi Arsula

are you running this through recon-all or outside of it? The skull 
stripping works better after the intensity normalization  that is part of 
recon-all


cheers
Bruce


On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:

 
 Hello,
 
 
 I’m new with FreeSurfer and I’m getting a really bad skull stripping (almo

st
 nothing) with mri_watershed –atlas in images converted from DICOM to .mgz
 with mri_convert. I lowered the threshold but did not improved considerabl
y.
 I have tried with a subject from the tutorial dataset and it’s OK. What ca
n
 be the problem?
 
 Thank you very much!
 
 
 Úrsula
 
 



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[Freesurfer] mri_watershed error, White Matter Intensity too high

[shahrzad kharabian]

Dear experts, 

I have a encountered an Error while doing skull-stripping using freesurfer on 
my T1 weighted images, using mri_watershed

I am using the following command:

mri_watershed -atlas mprage_RPI.mgz mprage_skullstrip.mgz

and here is the error:

mri_watershed Error: 
w=White Matter =Intensity too high (240)...valid input ?

I checked the images, actualy White matter intensity is around 300 . 


How could I overcome this issue?


Bests, 

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Re: [Freesurfer] mri_watershed and other errors.

[Darren Gitelman]

OK. So do you have any other suggestions? Is there some minor difference
between my version and yours that would explain this behavior. Other
settings to try?

Darren

On Wed, Sep 5, 2012 at 4:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 our internal development version.
 On Wed, 5 Sep 2012, Darren Gitelman
 wrote:

  Bruce
  I used the following
  version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
 
  Is that the same as the one you are using or are you referring to an
  internal development version?
 
  I will try Nick's suggestion as well.
 
  Darren
 
  On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 
  wrote:
I'm running it now with the current dev version and it's passed
the skull
stripping stage and it seems to have worked fine...
 
On Wed,
5 Sep 2012, Nick Schmansky wrote:
 
 Darren,

 I forgot to mention that you'll need to add

 -clean-bm

 after the -no-wsgcaatlas flag, otherwise the prior
brainmask.mgz will be
 retained and the new one will be saved as brainmask.auto.mgz.

 Nick


 On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
   Nick, List:
  
  
  
   Still no luck with this data. See attached as an example.
  
  
  
   To get to this point I had run:
  
  
  
   recon-all -all
  
  
  
   This ran to the error: mri_watershed Error:   GLOBAL region of the
   brain empty !
  
  
  
   Then I followed your recommendation below
  
  
  
   recon-all -s  subjid -skullstrip -no-wsgcaatlas, which had no
  errors
   and then
  
   recon-all -s subjid -autorecon2 -autorecon3
  
  
  
   This produced the result attached.
  
  
  
   I then deleted this directory and re-imported all the dicom data
  for
   this subject. Looked at the images, which look fine.
  
   Then I ran recon-all -s subjid -autorecon1
  
  
  
   This fails with the mri_watershed error.
  
  
  
   Then I ran recon-all -s  subjid -skullstrip -no-wsgcaatlas.
  
  
  
   This runs without error but when I look at the brainmask.mgz it
  looks
   just like the attached image.
  
  
  
   Is there some way to set the thresholds differently? The T1 image
   looks fine to me although perhaps the intensity is slightly less
  than
   usual, but it doesn't seem particularly noisy.
  
  
  
   Darren
  
  
  
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  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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  Northwestern University
  710 N. Lake Shore Dr.
  Abbott 11th Floor
  Chicago, IL 60611
  Ph: (312) 908-8614
  Fax: (312) 908-5073
 
 
 
 




-- 
Darren Gitelman, MD
Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073
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Re: [Freesurfer] mri_watershed and other errors.

[Darren Gitelman]

Nick, List:



Still no luck with this data. See attached as an example.



To get to this point I had run:



recon-all -all



This ran to the error: mri_watershed Error:   GLOBAL region of the brain
empty !



Then I followed your recommendation below



recon-all -s  subjid -skullstrip -no-wsgcaatlas, which had no errors and
then

recon-all -s subjid -autorecon2 -autorecon3



This produced the result attached.



I then deleted this directory and re-imported all the dicom data for this
subject. Looked at the images, which look fine.

Then I ran recon-all -s subjid -autorecon1



This fails with the mri_watershed error.



Then I ran recon-all -s  subjid -skullstrip -no-wsgcaatlas.



This runs without error but when I look at the brainmask.mgz it looks just
like the attached image.



Is there some way to set the thresholds differently? The T1 image looks
fine to me although perhaps the intensity is slightly less than usual, but
it doesn't seem particularly noisy.



Darren
attachment: FS_error.jpg___
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Re: [Freesurfer] mri_watershed and other errors.

[Bruce Fischl]

Hi Darren

can you describe your input data? What format, resolution, etc... is it? 
If you upload it we'll take a look

cheers
Bruce
On Wed, 5 Sep 2012, Darren Gitelman 
wrote:




Nick, List:

 

Still no luck with this data. See attached as an example. 

 

To get to this point I had run:

 

recon-all -all 

 

This ran to the error: mri_watershed Error:   GLOBAL region of the brain empty !

 

Then I followed your recommendation below

 

recon-all -s  subjid -skullstrip -no-wsgcaatlas, which had no errors and then

recon-all -s subjid -autorecon2 -autorecon3

 

This produced the result attached.

 

I then deleted this directory and re-imported all the dicom data for this 
subject. Looked at the images, which look fine.

Then I ran recon-all -s subjid -autorecon1

 

This fails with the mri_watershed error.

 

Then I ran recon-all -s  subjid -skullstrip -no-wsgcaatlas.

 

This runs without error but when I look at the brainmask.mgz it looks just like 
the attached image.

 

Is there some way to set the thresholds differently? The T1 image looks fine to 
me although perhaps the intensity is slightly
less than usual, but it doesn't seem particularly noisy.

 

Darren

 


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Re: [Freesurfer] mri_watershed and other errors.

[Darren Gitelman]

Bruce:

Thank you for looking. I have uploaded the files:
I uploaded them in Dicom Format.
This is a T1, MPRAGE, image, acquired with GRAPPA, resolution 1x1x1.
Name: 3157.tar.gz

Darren



On Wed, Sep 5, 2012 at 11:27 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 Hi Darren

 can you describe your input data? What format, resolution, etc... is it?
 If you upload it we'll take a look
 cheers
 Bruce
 On Wed, 5 Sep 2012, Darren Gitelman
 wrote:

 
  Nick, List:
 
 
 
  Still no luck with this data. See attached as an example.
 
 
 
  To get to this point I had run:
 
 
 
  recon-all -all
 
 
 
  This ran to the error: mri_watershed Error:   GLOBAL region of the brain
 empty !
 
 
 
  Then I followed your recommendation below
 
 
 
  recon-all -s  subjid -skullstrip -no-wsgcaatlas, which had no errors
 and then
 
  recon-all -s subjid -autorecon2 -autorecon3
 
 
 
  This produced the result attached.
 
 
 
  I then deleted this directory and re-imported all the dicom data for
 this subject. Looked at the images, which look fine.
 
  Then I ran recon-all -s subjid -autorecon1
 
 
 
  This fails with the mri_watershed error.
 
 
 
  Then I ran recon-all -s  subjid -skullstrip -no-wsgcaatlas.
 
 
 
  This runs without error but when I look at the brainmask.mgz it looks
 just like the attached image.
 
 
 
  Is there some way to set the thresholds differently? The T1 image looks
 fine to me although perhaps the intensity is slightly
  less than usual, but it doesn't seem particularly noisy.
 
 
 
  Darren
 
 
 
 
 


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 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
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 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




-- 
Darren Gitelman, MD
Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073
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Re: [Freesurfer] mri_watershed and other errors.

[Nick Schmansky]

Darren,

I forgot to mention that you'll need to add 

-clean-bm

after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
retained and the new one will be saved as brainmask.auto.mgz.

Nick


On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
 Nick, List:
 
  
 
 Still no luck with this data. See attached as an example. 
 
  
 
 To get to this point I had run:
 
  
 
 recon-all -all 
 
  
 
 This ran to the error: mri_watershed Error:   GLOBAL region of the
 brain empty !
 
  
 
 Then I followed your recommendation below
 
  
 
 recon-all -s  subjid -skullstrip -no-wsgcaatlas, which had no errors
 and then
 
 recon-all -s subjid -autorecon2 -autorecon3
 
  
 
 This produced the result attached.
 
  
 
 I then deleted this directory and re-imported all the dicom data for
 this subject. Looked at the images, which look fine.
 
 Then I ran recon-all -s subjid -autorecon1
 
  
 
 This fails with the mri_watershed error.
 
  
 
 Then I ran recon-all -s  subjid -skullstrip -no-wsgcaatlas.
 
  
 
 This runs without error but when I look at the brainmask.mgz it looks
 just like the attached image.
 
  
 
 Is there some way to set the thresholds differently? The T1 image
 looks fine to me although perhaps the intensity is slightly less than
 usual, but it doesn't seem particularly noisy.
 
  
 
 Darren
 
  
 
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Re: [Freesurfer] mri_watershed and other errors.

[Bruce Fischl]

I'm running it now with the current dev version and it's passed the skull 
stripping stage and it seems to have worked fine...

On Wed, 
5 Sep 2012, Nick Schmansky wrote:

 Darren,

 I forgot to mention that you'll need to add

 -clean-bm

 after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
 retained and the new one will be saved as brainmask.auto.mgz.

 Nick


 On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
 Nick, List:



 Still no luck with this data. See attached as an example.



 To get to this point I had run:



 recon-all -all



 This ran to the error: mri_watershed Error:   GLOBAL region of the
 brain empty !



 Then I followed your recommendation below



 recon-all -s  subjid -skullstrip -no-wsgcaatlas, which had no errors
 and then

 recon-all -s subjid -autorecon2 -autorecon3



 This produced the result attached.



 I then deleted this directory and re-imported all the dicom data for
 this subject. Looked at the images, which look fine.

 Then I ran recon-all -s subjid -autorecon1



 This fails with the mri_watershed error.



 Then I ran recon-all -s  subjid -skullstrip -no-wsgcaatlas.



 This runs without error but when I look at the brainmask.mgz it looks
 just like the attached image.



 Is there some way to set the thresholds differently? The T1 image
 looks fine to me although perhaps the intensity is slightly less than
 usual, but it doesn't seem particularly noisy.



 Darren



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Re: [Freesurfer] mri_watershed and other errors.

[Darren Gitelman]

Bruce

I used the following
version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522

Is that the same as the one you are using or are you referring to an
internal development version?

I will try Nick's suggestion as well.

Darren

On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 I'm running it now with the current dev version and it's passed the skull
 stripping stage and it seems to have worked fine...

 On Wed,
 5 Sep 2012, Nick Schmansky wrote:

  Darren,
 
  I forgot to mention that you'll need to add
 
  -clean-bm
 
  after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
  retained and the new one will be saved as brainmask.auto.mgz.
 
  Nick
 
 
  On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
  Nick, List:
 
 
 
  Still no luck with this data. See attached as an example.
 
 
 
  To get to this point I had run:
 
 
 
  recon-all -all
 
 
 
  This ran to the error: mri_watershed Error:   GLOBAL region of the
  brain empty !
 
 
 
  Then I followed your recommendation below
 
 
 
  recon-all -s  subjid -skullstrip -no-wsgcaatlas, which had no errors
  and then
 
  recon-all -s subjid -autorecon2 -autorecon3
 
 
 
  This produced the result attached.
 
 
 
  I then deleted this directory and re-imported all the dicom data for
  this subject. Looked at the images, which look fine.
 
  Then I ran recon-all -s subjid -autorecon1
 
 
 
  This fails with the mri_watershed error.
 
 
 
  Then I ran recon-all -s  subjid -skullstrip -no-wsgcaatlas.
 
 
 
  This runs without error but when I look at the brainmask.mgz it looks
  just like the attached image.
 
 
 
  Is there some way to set the thresholds differently? The T1 image
  looks fine to me although perhaps the intensity is slightly less than
  usual, but it doesn't seem particularly noisy.
 
 
 
  Darren
 
 
 
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Ph: (312) 908-8614
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Re: [Freesurfer] mri_watershed and other errors.

[Darren Gitelman]

Nick

I ran:  recon-all -skullstrip -no-wsgcaatlas -clean-bm -s 3157

and got the exact same problem with brainmask.mgz

Darren

On Wed, Sep 5, 2012 at 3:37 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote:

 Darren,

 I forgot to mention that you'll need to add

 -clean-bm

 after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
 retained and the new one will be saved as brainmask.auto.mgz.

 Nick


 On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
  Nick, List:
 
 
 
  Still no luck with this data. See attached as an example.
 
 
 
  To get to this point I had run:
 
 
 
  recon-all -all
 
 
 
  This ran to the error: mri_watershed Error:   GLOBAL region of the
  brain empty !
 
 
 
  Then I followed your recommendation below
 
 
 
  recon-all -s  subjid -skullstrip -no-wsgcaatlas, which had no errors
  and then
 
  recon-all -s subjid -autorecon2 -autorecon3
 
 
 
  This produced the result attached.
 
 
 
  I then deleted this directory and re-imported all the dicom data for
  this subject. Looked at the images, which look fine.
 
  Then I ran recon-all -s subjid -autorecon1
 
 
 
  This fails with the mri_watershed error.
 
 
 
  Then I ran recon-all -s  subjid -skullstrip -no-wsgcaatlas.
 
 
 
  This runs without error but when I look at the brainmask.mgz it looks
  just like the attached image.
 
 
 
  Is there some way to set the thresholds differently? The T1 image
  looks fine to me although perhaps the intensity is slightly less than
  usual, but it doesn't seem particularly noisy.
 
 
 
  Darren
 
 
 
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Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073
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Re: [Freesurfer] mri_watershed and other errors.

[Bruce Fischl]

our internal development version.
On Wed, 5 Sep 2012, Darren Gitelman 
wrote:



Bruce
I used the following
version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522

Is that the same as the one you are using or are you referring to an
internal development version?

I will try Nick's suggestion as well.

Darren

On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
  I'm running it now with the current dev version and it's passed
  the skull
  stripping stage and it seems to have worked fine...

  On Wed,
  5 Sep 2012, Nick Schmansky wrote:

   Darren,
  
   I forgot to mention that you'll need to add
  
   -clean-bm
  
   after the -no-wsgcaatlas flag, otherwise the prior
  brainmask.mgz will be
   retained and the new one will be saved as brainmask.auto.mgz.
  
   Nick
  
  
   On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
 Nick, List:



 Still no luck with this data. See attached as an example.



 To get to this point I had run:



 recon-all -all



 This ran to the error: mri_watershed Error:   GLOBAL region of the
 brain empty !



 Then I followed your recommendation below



 recon-all -s  subjid -skullstrip -no-wsgcaatlas, which had no
errors
 and then

 recon-all -s subjid -autorecon2 -autorecon3



 This produced the result attached.



 I then deleted this directory and re-imported all the dicom data
for
 this subject. Looked at the images, which look fine.

 Then I ran recon-all -s subjid -autorecon1



 This fails with the mri_watershed error.



 Then I ran recon-all -s  subjid -skullstrip -no-wsgcaatlas.



 This runs without error but when I look at the brainmask.mgz it
looks
 just like the attached image.



 Is there some way to set the thresholds differently? The T1 image
 looks fine to me although perhaps the intensity is slightly less
than
 usual, but it doesn't seem particularly noisy.



 Darren



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--
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Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073



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Re: [Freesurfer] mri_watershed and other errors.

[Nick Schmansky]

try running:

recon-all -s subjid -skullstrip -no-wsgcaatlas 

if that works, continue the rest with:

recon-all -s subjid -autorecon2 -autorecon3

n.


On Wed, 2012-08-29 at 17:01 +, Darren R Gitelman wrote:
 Hi
 
 I am having a problem getting recon-all to finish on 1 subject. 
 
 The first time I ran recon-all -all I got an mri_watershed error. (see
 attached log).
 
 Based on one of the posts to the list I then ran:
 recon-all -skullstrip -no-wsgcaatlas -s subj id
 
 This completed successfully.
 Then I ran:
 recon-all -autorecon2 -autorecon3 -s subj id
 
 This did not complete successfully with the error that it can't find
 the brain.mgz file.
 I did look at the orig.mgz and T1.mgz files and they look fine. The
 talairach transform I think is also fine.
 
 What do I do about this?
 
 Thanks,
 Darren
 
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Re: [Freesurfer] mri_watershed for inner_skull_surface question

[Roderick McColl]

Hi Bruce,
Thanks for responding.
We do have T2, but not PD. 
Of course the resolution of the T2 is much lower (5mm slices). 
-roddy

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Wednesday, September 21, 2011 7:54 AM
To: Roderick McColl; Matti Hamalainen
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed for inner_skull_surface question

Matti Hamalainen (ccd) might have some thoughts. Do you have T2 or PD images?

cheers
Bruce

On Tue, 20 Sep 2011, Roderick McColl wrote:

 Hi all,
  
 Trying to get mri_watershed to give me a good inner_skull_surface, 
 which I want to combine with the pial surface to estimate sulcal CSF, 
 as I don't see any other way. Unfortunately the data I have tested on 
 all generate unreliable inner_skull surfaces. Can anyone provide a tip for 
 optimizing the result?
  
 Thanks
  
 -roddy
  
 
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 __
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 The future of medicine, today.
 



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Re: [Freesurfer] mri_watershed for inner_skull_surface question

[Bruce Fischl]

Matti Hamalainen (ccd) might have some thoughts. Do you have T2 or PD 
images?


cheers
Bruce

On Tue, 20 Sep 2011, Roderick McColl wrote:


Hi all,
 
Trying to get mri_watershed to give me a good inner_skull_surface, which I want
to combine with the pial surface to estimate sulcal CSF, as I don't see any
other way. Unfortunately the data I have tested on all generate unreliable
inner_skull surfaces. Can anyone provide a tip for optimizing the result?
 
Thanks
 
-roddy
 

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[Freesurfer] mri_watershed for inner_skull_surface question

[Roderick McColl]

Hi all,

Trying to get mri_watershed to give me a good inner_skull_surface, which I want
to combine with the pial surface to estimate sulcal CSF, as I don't see any
other way. Unfortunately the data I have tested on all generate unreliable
inner_skull surfaces. Can anyone provide a tip for optimizing the result?

Thanks

-roddy




UT Southwestern Medical Center
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[Freesurfer] mri_watershed for generating scalp surfaces

[Vema Krishnamurthy, Santosh]

Hello Everyone,

I have an application outside freesurfer where I need the scalp/face surface 
from the MRI file so I'm trying to use mri_watershed algorithm to generate the 
scalp surface, but when I read the subject-outer_skin.surf file in matlab using 
the read_surf command I see that the facial features (nose, eyes, lips, chin) 
are not clear. But when I viewed the MRI file using mrilab I can see the facial 
features clearly. So I was wondering if there are parameters I can change while 
running the mri_watershed alrgorithm so that I can get good face shape. I'm 
also up for any suggestions/hints.

Here is the command I used to run the mri_watershed:
mri_watershed -atlas -useSRAS -surf /../../bem/watershed/subject 
/../..subject/T1.mgz /../../bem/watershed/ws/

Thanks and Regards,
---
Santosh Vema KrishnaMurthy, M.A.Sc
Medical Devices Engineer
NRC Institute for Biodiagnostics (Atlantic)
Elekta/IWK MEG Research office
Ph: (902) 470-3984
---
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Re: [Freesurfer] mri_watershed for generating scalp surfaces

[Douglas N Greve]

You can try using mkheadsurf. Run it with --help to get more info.
doug

Vema Krishnamurthy, Santosh wrote:
 Hello Everyone,
  
 I have an application outside freesurfer where I need the scalp/face 
 surface from the MRI file so I'm trying to use mri_watershed algorithm 
 to generate the scalp surface, but when I read the 
 subject-outer_skin.surf file in matlab using the read_surf command I 
 see that the facial features (nose, eyes, lips, chin) are not clear. 
 But when I viewed the MRI file using mrilab I can see the facial 
 features clearly. So I was wondering if there are parameters I can 
 change while running the mri_watershed alrgorithm so that I can 
 get good face shape. I'm also up for any suggestions/hints.
  
 Here is the command I used to run the mri_watershed:
 mri_watershed -atlas -useSRAS -surf /../../bem/watershed/subject 
 /../..subject/T1.mgz /../../bem/watershed/ws/
  
 Thanks and Regards,
 ---
 Santosh Vema KrishnaMurthy, M.A.Sc
 Medical Devices Engineer
 NRC Institute for Biodiagnostics (Atlantic)
 Elekta/IWK MEG Research office
 Ph: (902) 470-3984
 ---
 

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[Freesurfer] mri_watershed Error

[Shugao Xia]

Hi,

I ran recon-all on one subject,  and exited with errors:

mri_watershed Error:  GLOBAL region of the brain empty!

what is the reason which caused this error? Thank you in advance

Best

Shugao
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Re: [Freesurfer] mri_watershed Error

[Bruce Fischl]

can you check the talairach xform and see if it's ok?
On Thu, 23 Sep 2010, 
Shugao Xia wrote:

 Hi,

 I ran recon-all on one subject,  and exited with errors:

 mri_watershed Error:  GLOBAL region of the brain empty!

 what is the reason which caused this error? Thank you in advance

 Best

 Shugao

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Re: [Freesurfer] mri_watershed Error

[Nick Schmansky]

you could also try adding the -no-wsgcaatlas flag to the end of
recon-all.  but also make sure that the T1.mgz is not junk.

n.

On Thu, 2010-09-23 at 12:06 -0400, Bruce Fischl wrote:
 can you check the talairach xform and see if it's ok?
 On Thu, 23 Sep 2010, 
 Shugao Xia wrote:
 
  Hi,
 
  I ran recon-all on one subject,  and exited with errors:
 
  mri_watershed Error:  GLOBAL region of the brain empty!
 
  what is the reason which caused this error? Thank you in advance
 
  Best
 
  Shugao
 
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[Freesurfer] mri_watershed error

[Toh Hock Wong]

Dear freesurfer experts,
I need your help on recon. I tried to perform recon-all on my  
anonymized control subjects (chunk of face/eyes removed on T1.mgz) and  
run autorecon1.
   It ran smoothly till the end of workflow of autorecon1 and came up  
with the following:
   mri_watershed Error:
   GLOBAL region of the brain empty!

   It then exited without compiling brainmask.mgz file.

   What should i try from here!

   Thanks for your help!
   Toh Wong
   Sydney, Australia

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Re: [Freesurfer] mri_watershed error

[Bruce Fischl]

Hi Toh,

did you check the talairach transform? If it's ok, try either running the 
watershed skull stripping with a different preflooding height or without 
the atlas.

cheers
Bruce


On Sat, 17 Jul 2010, Toh Hock Wong wrote:

 Dear freesurfer experts,
I need your help on recon. I tried to perform recon-all on my
 anonymized control subjects (chunk of face/eyes removed on T1.mgz) and
 run autorecon1.
   It ran smoothly till the end of workflow of autorecon1 and came up
 with the following:
   mri_watershed Error:
   GLOBAL region of the brain empty!

   It then exited without compiling brainmask.mgz file.

   What should i try from here!

   Thanks for your help!
   Toh Wong
   Sydney, Australia

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[Freesurfer] mri_watershed error

[Antoine Leflon]

Hi ,

I encountered an error during the watershed and I tried to check the  
disk space running : zcat  
/usr/local/freesurfer/subjects/s2/mri/T1.mgz  
/usr/local/freesurfer/subjects/s2/mri/T1.mgh
An image file appeared but it is impossible to open it because it has  
a width of zero .
what does it mean ?

thanks ,

Antoine Leflon

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Re: [Freesurfer] mri_watershed and mri_make_bem_surfaces

[Bruce Fischl]

Hi Andres,

those errors are probably not related (tkmedit tries to read an array of 
cortical surfaces that don't exist for the BEM analysis). I'm not sure what 
BEM mesh editing tools exist - maybe Matti knows?


cheers,
Bruce


 On Wed, 3 Mar 2010, Andres Felipe Salazar Gomez wrote:


Hello FreeSurfer users,

I am using a set of MNE commands (mne_watershed_bem and mne_flash_bem)
that call respectively mri_watershed and mri_make_bem_surfaces to create
the BEM surfaces. I am having problems when checking one of them, the
inner_skull mesh, since in several subjects, when visualized on tkmedit,
it appears to be going not along the edge of the gray matter but inside
it, specially at the occipital lobe level.

Has anyone had a similar problem? How can the inner_skull file be modified?

I found an error log file with the following info but I do not know if it
is related to the problem.

MRISreadVertexPosition(orig): could not open file
$SUBJECTS_DIR/$SUBJECT/bem/flash/lh.orig
MRISreadVertexPosition(pial): could not open file
SUBJECTS_DIR/$SUBJECT/bem/flash/lh.pial

I appreciate any help in this matter.

Thank you,

-- Andrés



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[Freesurfer] mri_watershed and mri_make_bem_surfaces

[Andres Felipe Salazar Gomez]

Hello FreeSurfer users,

I am using a set of MNE commands (mne_watershed_bem and mne_flash_bem)
that call respectively mri_watershed and mri_make_bem_surfaces to create
the BEM surfaces. I am having problems when checking one of them, the
inner_skull mesh, since in several subjects, when visualized on tkmedit,
it appears to be going not along the edge of the gray matter but inside
it, specially at the occipital lobe level.

Has anyone had a similar problem? How can the inner_skull file be modified?

I found an error log file with the following info but I do not know if it
is related to the problem.

MRISreadVertexPosition(orig): could not open file
$SUBJECTS_DIR/$SUBJECT/bem/flash/lh.orig
MRISreadVertexPosition(pial): could not open file
SUBJECTS_DIR/$SUBJECT/bem/flash/lh.pial

I appreciate any help in this matter.

Thank you,

-- Andrés



-- 
Andres F. Salazar
Research Technologist
Neuroscience Statistics Research Laboratory
asala...@nmr.mgh.harvard.edu
149 13th Street, Room 4005
Charlestown, MA  02129



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[Freesurfer] mrI_watershed volume segmentation

[slew]

Hi,

I used mri_watershed to get volume segmenstation with -LABEL option.

mri_watershed -atlas -LABEL $SUBJECTS_DIR/test/mri/T1.mgz
$SUBJECTS_DIR/test/tmp/

What coordinate system is used for the segmented volume ? The coordinate
seems a lot different from that of the surface extraction with SRAS.  Is
RAS coordinate used for the volume segmentation? Is there a way to
transform the segmented volume to SRAS ?

Thanks,
Seok


-- 
Seok Lew, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Building 149, 13th Street, Mailcode 149-2301
Charlestown, MA 02129-2060
USA

e-mail  s...@nmr.mgh.harvard.edu
FAX 617 726 7422



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[Freesurfer] mri_watershed error

[Kathy Zhang]

Hello all,

I've been working with a set of about 200 brains, and in 19 of these I'm
getting the error mri_watershed Error: GLOBAL region of the brain empty
!.  I've checked the talairach transformation with tkregister2, and in 17
of those cases, the transformations look fine (the two other cases were just
bad scans).  I'm using freesurfer version 4.0.5 for linux, and have already
tried previous suggestions to run a skull strip off orig.mgz and checking
the FOV values on T1.mgz and orig.mgz.

Does anyone know what I could do to fix this error or somehow work around it
to continue the skull strip?

Thanks,
Kathy Zhang
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Re: [Freesurfer] mri_watershed error

[Nick Schmansky]

Kathy,

Can you send me the 001.mgz file for one of these subjects?  Send it via
the filedrop:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

The 001.mgz file is in the subj/mri/orig directory (and you might have
a 002.mgz file as well, if you had two structurals for this subject).

Nick



On Thu, 2009-02-05 at 14:59 -0500, Kathy Zhang wrote:
 Hello all, 
 
 I've been working with a set of about 200 brains, and in 19 of these
 I'm getting the error mri_watershed Error: GLOBAL region of the brain
 empty !.  I've checked the talairach transformation with tkregister2,
 and in 17 of those cases, the transformations look fine (the two other
 cases were just bad scans).  I'm using freesurfer version 4.0.5 for
 linux, and have already tried previous suggestions to run a skull
 strip off orig.mgz and checking the FOV values on T1.mgz and orig.mgz.
 
 Does anyone know what I could do to fix this error or somehow work
 around it to continue the skull strip?
 
 Thanks,
 Kathy Zhang
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Re: [Freesurfer] mri_watershed regions appearing round edge, freesurfer 4.0.2

[Bruce Fischl]

Hi Ian,

does this mess up the ?h.white or ?h.pial surfaces? Or the aseg.mgz? If 
not, I wouldn't worry about it.


cheers,
Bruce
On Tue, 5 Aug 2008, Ian Malone wrote:

To illustrate the issue, this is a slice from one of the problematic volumes. 
The blue outlines surround non-zero voxels, the regions around the edges 
carry on parallel to those planes.


Ian

Ian Malone wrote:
It's not terrible; it can be worked around.  But it does feel more like a 
bug than a feature, as these voxels are un-connected with any in the brain. 
It looks a bit like the edge of a bounding box.


Thanks,
Ian

Bruce Fischl wrote:

Hi Ian,

mri_watershed minimizes a risk functional in which we weigh the cost of 
leaving non-brain voxels to be much less than stripping true brain ones, 
so it does sometimes leave stuff around. Is this causing any problems?


Bruce
On Wed, 30 Jul 2008, Ian Malone wrote:


Hi,

Has anyone encountered this before?  I have a few volumes for which 
mri_watershed output volumes are fine apart from some non-zero voxels 
near the edges (which are not connected to the brain).  The volumes are 
in transverse format and the most noticeable effect is some inferior 
slices (neck, lower jaw) which are not being masked out, though there are 
also some voxels close to the coronal edges. For both sets of edges there 
is a one or two voxel thick layer parallel to either the coronal or 
transverse plane.


This is with Freesurfer 4.0.2, T1 images in Analyze format.

Thanks for your time,
Ian Malone
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Re: [Freesurfer] mri_watershed regions appearing round edge, freesurfer 4.0.2

[Bruce Fischl]

Hi Ian,

mri_watershed minimizes a risk functional in which we weigh the cost of 
leaving non-brain voxels to be much less than stripping true brain ones, 
so it does sometimes leave stuff around. Is this causing any problems?


Bruce
On 
Wed, 30 Jul 2008, Ian Malone wrote:



Hi,

Has anyone encountered this before?  I have a few volumes for which 
mri_watershed output volumes are fine apart from some non-zero voxels near 
the edges (which are not connected to the brain).  The volumes are in 
transverse format and the most noticeable effect is some inferior slices 
(neck, lower jaw) which are not being masked out, though there are also some 
voxels close to the coronal edges. For both sets of edges there is a one or 
two voxel thick layer parallel to either the coronal or transverse plane.


This is with Freesurfer 4.0.2, T1 images in Analyze format.

Thanks for your time,
Ian Malone
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[Freesurfer] mri_watershed Error: Problem with WM_HALF_MIN too small

[Gonzalo Sanchez Benavides]

Dear FS experts,

When I run recon-all, one of my subjects get this error in mri_watershed
process:

*WATERSHED**
Sorting...
  first estimation of the COG coord: x=121 y=125 z=133 r=78
  first estimation of the main basin volume: 2032411 voxels
mri_watershed Error:
 Problem with WM_HALF_MIN too small

Can you tell me what's wrong? The input image seems to be good enough.

Thank you very much for your answers and for this excellent software


-- 
Gonzalo Sánchez Benavides
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[Freesurfer] mri_watershed: distorted inner skull surface

[Silviu Podariu]

Hi,

In order to get the three BEMs for EEG/MEG 3D source reconstruction 
for subject X, I used mri_watershed with -atlas, -useSRAS and -surf
options, which created the BEMs in X/bem/watershed/, but the
inner_skull and the brain were significantly distorted.

I followed the tutorial on troubleshooting the surfaces in the X/surf/
folder, but that does not address fixing these BEMs, so I was
wondering if anybody knows how to get around this problem. 

Actually, what concerns us most is if it's possible to get at least
the inner skull surface right, as we shall be using the pial surface
in X/surf/ (downsampled from 150k vertices) for the brain instead of
the mri_watershed output (but I did not find there an inner skull
surface). 

Thank you,

Silviu Podariu
UNMC
Omaha, NE
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RE: [Freesurfer] mri_watershed - BEM surfaces problem

[Don Hagler]

matlab's reducepatch
Date: Thu, 10 Apr 2008 10:39:37 -0700
From: [EMAIL PROTECTED]
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed - BEM surfaces problem

P.S.  Also, I was wondering if there is a utility to reduce the number
of vertices of a given surface (i.e. to make a less precise
triangulation) at will. I
 thought I may use the pial left and right 
halves greatly reduced (from about 140k vertices to 10k or less) for
the brain surface instead of the mri_watershed output. 

  
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[Freesurfer] mri_watershed - BEM surfaces problem

[Silviu Podariu]

Hi,

In order to get the three BEMs for 3D source reconstruction for
subject X, I used: 

mri_watershed   -atlas   -useSRAS   -surf   X/bem/watershed/X
X/mri/T1.mgz   X/bem/watershed/ws

which created the BEMs in X/bem/watershed/, but the inner_skull and
the brain were significantly distorted, mainly on the left side (the
scalp BEM is okay).  

I followed the tutorial on troubleshooting the surfaces in the X/surf/
folder, but that does not address fixing these BEMs, so I was
wondering if anybody knows how to get around this problem (should I
edit the T1.mgz volume and run again?). 

Thank you,

Silviu Podariu
UNMC
Omaha, NE

P.S.  Also, I was wondering if there is a utility to reduce the number
of vertices of a given surface (i.e. to make a less precise
triangulation) at will. I thought I may use the pial left and right 
halves greatly reduced (from about 140k vertices to 10k or less) for
the brain surface instead of the mri_watershed output. 

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Re: [Freesurfer] mri_watershed Error: GLOBAL region of the brain empty

[Bruce Fischl]

Hi Ozlem,

if it's the talairach_with_skull.lta as described previously. I have a fix 
for it that will be in the upcoming stable. In the interim you could try 
running watershed without the talaiarch_with_skull.lta


cheers,
Bruce



Hello,

I have the same error (mri_watershed Error: GLOBAL region of the brain empty
!) as described Micheal Harms' mail (below) which left I guessed as
unanswered. Any help would be appreciated.

Thanks,

Ozlem OZMEN-OKUR
Bogazici Univ. Biomedical Engineering
Istanbul-TURKEY
[Freesurfer] autorecon1 errors

Michael Harms
Tue, 26 Feb 2008 13:31:48 -0800

Hello,
We recently just ran 80 elderly brains through -autorecon1 using FS
v4.0.2, and encountered 3 different types of errors that we are not
entirely sure how to handle:

(1) During mri_normalize of 1 subject we encountered:

SPLINE_CUBIC_SET - Fatal error!
 The number of data points N must be at least 2.
 The input value is 1.

The FS archive indicates to check the talairach transform given this
error, but the talairach.xfm appears fine for this subject (as assessed

using tkregister2).

(2) During mri_watershed of 1 subject:
Sorting...
mri_watershed Error:
Problem in the COG calculation

This subject had a slightly warped talaraich.xfm, but I think more
relevantly, its talairach_with_skull.lta was way off.


(3) During mri_watershed of 5 subjects:
mri_watershed Error:
GLOBAL region of the brain empty !

For all 5 of these subjects, the talairch_with_skull.lta also had
obvious problems.

RE (1): Any insight would be appreciated.


RE (2) and (3): I suspect that we should try running with the -no-
wsgcaatlas flag, so that talairach_with_skull.lta is longer used by
mri_watershed.  Should we then substitute the -wsatlas flag instead?
(Its not clear to me which atlas is used when that particular flag is

included).

Last, I thought you might be interested in these errors, because they
directly relate to my recent question regarding the robustness of
talairach_with_skull.lta.  At least during the -autorecon1 (i.e.,

initial) creation of this lta file, it appears that there is some
possibility of a bad talairach_with_skull registration (6 of 80 in this
particular subject set).

thanks,
Mike H.


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[Freesurfer] mri_watershed problem

[Cameron Ellis]

Hi everyone,
I am trying to output bem surfaces using mri_watershed and I receive badly
distorted surfaces. During the autorecon process there did not appear to
be any errors generated, and the final surfaces look good, it is just in
producing the bem surfaces independent from autorecon that errors arise. I
am trying to get any information as to why these surfaces would come out
distorted and potential correction strategies. Any advice is much
appreciated!
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[Freesurfer] mri_watershed

[nima]

hi,
Under freesurfer, how can I force mri_watershed to create 5012 triangles
(ico 4) instead of 20480?
cheers
nima


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Re: [Freesurfer] mri_watershed

[Nick Schmansky]

Nima,

There is no flag to mri_watershed to allow this, but you can trick it by
doing the following:

  cd $FREESURFER_HOME/lib/bem
  mv ic5.tri ic5.bak
  ln -s ic4.tri ic5.tri

This will force usage of ic4.tri, which has 5120 triangles.

Nick

On Wed, 2007-08-08 at 17:46 -0400, [EMAIL PROTECTED] wrote:
 hi,
 Under freesurfer, how can I force mri_watershed to create 5012 triangles
 (ico 4) instead of 20480?
 cheers
 nima
 
 
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[Freesurfer] mri_watershed question

[Avram Holmes]

All,

I am interested in using mri_watershed to remove the skull from an inplane
low res structural scan (not an MPRAGE). However, when I try to I get the
following message followed by the program crashing.


Mode:  Atlas analysis

*
The input file is P1.mgz
The output file is brainmask.auto.mgz
If this is incorrect, please exit with CTL-C

changing type of input volume to 8 bits/voxel...
MRIchangeType: Building histogram

*WATERSHED**
preflooding height equal to 25 percent
Sorting...
  first estimation of the COG coord: x=127 y=133 z=24 r=80
  first estimation of the main basin volume: 2160181
voxelsSegmentation fault (core dumped)

I am sure that I am missing some simple flag. Does anyone know a solution
to this before I run off and start using BET.

Thanks,
Avram
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Re: [Freesurfer] mri_watershed question

[Bruce Fischl]

Hi Avram,

not sure if it will work, but it certainly shouldn't crash. If you put 
the data somewhere I can get it (e.g. on our filedrop) I'll take a look.


cheers,
Bruce
On 
Wed, 2 Aug 2006, Avram Holmes wrote:



All,

I am interested in using mri_watershed to remove the skull from an inplane
low res structural scan (not an MPRAGE). However, when I try to I get the
following message followed by the program crashing.


Mode:  Atlas analysis

*
The input file is P1.mgz
The output file is brainmask.auto.mgz
If this is incorrect, please exit with CTL-C

changing type of input volume to 8 bits/voxel...
MRIchangeType: Building histogram

*WATERSHED**
preflooding height equal to 25 percent
Sorting...
 first estimation of the COG coord: x=127 y=133 z=24 r=80
 first estimation of the main basin volume: 2160181
voxelsSegmentation fault (core dumped)

I am sure that I am missing some simple flag. Does anyone know a solution
to this before I run off and start using BET.

Thanks,
Avram
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Re: [Freesurfer] mri_watershed

[Nick Schmansky]

or in your case dave, just:

  cp brainmask.mgz brainmask.auto.mgz

since you manually edited brainmask.mgz


On Thu, 2006-06-29 at 14:18 -0400, Doug Greve wrote:
 
 I'm not sure what will happen. Safest to just recreate it:
 
 cd subject/mri
 mri_watershed T1.mgz brainmask.auto.mgz
 
 
 [EMAIL PROTECTED] wrote: 
  Alright I converted the COR files to mgz fine, and saved the volume as
  brainmask.mgz.  All looks good.  But before I run -autorecon2, am I
  going to run into problems because I only have a brainmask.mgz and not a
  brainmask.auto.mgz?  (I deleted the old brainmask.auto.mgz because it
  was the old volumes before I corrected them manually).  I just want to
  make sure I am good to run -autorecon2 before I go ahead and begin it.
  
  Quoting Bruce Fischl [EMAIL PROTECTED]:
  

   but you'll need to convert the COR file you saved to brainmask.mgz if
   you 
   want to recover your edits (4 hours of manual editing!).
   
   Bruce
   
   On Wed, 28 Jun 
   2006, Nick Schmansky wrote:
   
   
The brainmask.mgz file is the one that should be edited (and
  
   saved), so
   
select that filename to save.  Then just continue with autorecon2
  
   (and
   
it will use your brainmask.mgz).  It will not overwrite your
brainmask.mgz unless you specify the aptly named '-clean-bm' flag
  
   to
   
recon-all.


On Wed, 2006-06-28 at 15:00 -0400, [EMAIL PROTECTED] wrote:
  
 I just finished my 4 hour manual editing...went to filesave
 
   volume
   
 as...then saved it to where it defaulted me, which was the mri
 
   folder of
   
 this subject.  When i pull up my brainmask, it is giving me the
 
   same one
   
 that it had before i made any changes.  I hope i didnt do
 
   something
   
 wrong and lost all the edits.  There is 256 COR files though now
 
   in my
   
 mri folder for this subject I noticed.  Maybe these are the
 
   edited
   
 slices?  Just let me know how to get my final brainmask and how
 
   to
   
 proceed with running -autorecon2 on it properly.  Thanks.
 
 Quoting Bruce Fischl [EMAIL PROTECTED]:
 
 
  it helps detect cases in which the deformation is too big (e.g.

   when
   
  the
  surface deforms all the way into the cerebellum), and can thus
  recover from
  e.g. cerebellum chopping.
  
  On
  Wed, 28 Jun 2006 [EMAIL PROTECTED] wrote:
  

   I am currently in the process of manual editing...just curious
   
  though,

   what exatly does adding an atlas do to the skullstrip process?
   
   Quoting Nick Schmansky [EMAIL PROTECTED]:
   
   
First have a look at the troubleshooting wiki pages at:


  
   https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
   
In particular, Subject 1 has a skull strip problem, and the
  
   fix
   
  info

is
here:


  
   https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
   
I'm guessing you have seen this page since you have already
attempted
one type of fix (adjusting the watershed parameters).  The
alternative
fix is the slice-by-slice manual editing.

You could also try adding the wsatlas flag:

  recon-all -s (subject) -skullstrip -wsatlas

which will use an atlas to help with the skull-strip.

Does the contrast of your image look good?  That is, comparing
  
  your

orig.mgz to that of the sample subject 'bert' included with
freesurfer?

Nick


On Wed, 2006-06-28 at 10:09 -0400, [EMAIL PROTECTED] wrote:
  
 I am having trouble with one of my skull strips, and getting
 
  very

 extreme results.  When I re-run the skullstrip using
 
   different
   
watershed
  
 values, anything at 56% or below takes 75%+ of the brain out,
 
  and

as
  
 soon as I jump to 57% or higher, it leaves on almost all of
 
   the
   
skull,
  
 except for maybe 5% of it.  Is this indicative of a more
 
complicated
  
 problem, and what is my next step (other than manually taking
 
  off

the
   

Re: [Freesurfer] mri_watershed

[Doug Greve]

Oh, don't do that! recon-all will compare the auto with the non-auto.
If they are the same then it will re-compute the auto and simply copy
to the non-auto, and your changes will be lost. If they are different,
then it will recompute the auto but will not propagate it to the
non-auto. Make sense?

doug



Nick Schmansky wrote:

  or in your case dave, just:

  cp brainmask.mgz brainmask.auto.mgz

since you manually edited brainmask.mgz


On Thu, 2006-06-29 at 14:18 -0400, Doug Greve wrote:
  
  
I'm not sure what will happen. Safest to just recreate it:

cd subject/mri
mri_watershed T1.mgz brainmask.auto.mgz


[EMAIL PROTECTED] wrote: 


  Alright I converted the COR files to mgz fine, and saved the volume as
brainmask.mgz.  All looks good.  But before I run -autorecon2, am I
going to run into problems because I only have a brainmask.mgz and not a
brainmask.auto.mgz?  (I deleted the old brainmask.auto.mgz because it
was the old volumes before I corrected them manually).  I just want to
make sure I am good to run -autorecon2 before I go ahead and begin it.

Quoting Bruce Fischl [EMAIL PROTECTED]:

  
  
  
but you'll need to convert the COR file you saved to brainmask.mgz if
you 
want to recover your edits (4 hours of manual editing!).

Bruce

On Wed, 28 Jun 
2006, Nick Schmansky wrote:




  The brainmask.mgz file is the one that should be edited (and
  
  

saved), so



  select that filename to save.  Then just continue with autorecon2
  
  

(and



  it will use your brainmask.mgz).  It will not overwrite your
brainmask.mgz unless you specify the aptly named '-clean-bm' flag
  
  

to



  recon-all.


On Wed, 2006-06-28 at 15:00 -0400, [EMAIL PROTECTED] wrote:
  
  
  
I just finished my 4 hour manual editing...went to filesave


  

volume



  
as...then saved it to where it defaulted me, which was the mri


  

folder of



  
this subject.  When i pull up my brainmask, it is giving me the


  

same one



  
that it had before i made any changes.  I hope i didnt do


  

something



  
wrong and lost all the edits.  There is 256 COR files though now


  

in my



  
mri folder for this subject I noticed.  Maybe these are the


  

edited



  
slices?  Just let me know how to get my final brainmask and how


  

to



  
proceed with running -autorecon2 on it properly.  Thanks.

Quoting Bruce Fischl [EMAIL PROTECTED]:




  it helps detect cases in which the deformation is too big (e.g.
  
  

  

when



  

  the
surface deforms all the way into the cerebellum), and can thus
recover from
e.g. cerebellum chopping.

On
Wed, 28 Jun 2006 [EMAIL PROTECTED] wrote:

  
  
  
I am currently in the process of manual editing...just curious


  
  though,
  
  
  
what exatly does adding an atlas do to the skullstrip process?

Quoting Nick Schmansky [EMAIL PROTECTED]:




  First have a look at the troubleshooting wiki pages at:


  
  

  

  

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData



  

  

  In particular, Subject 1 has a skull strip problem, and the
  
  

  

  

fix



  

  info
  
  
  

  is
here:


  
  

  

  

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix



  

  

  I'm guessing you have seen 

Re: [Freesurfer] mri_watershed

[Bruce Fischl]

it helps detect cases in which the deformation is too big (e.g. when the 
surface deforms all the way into the cerebellum), and can thus recover from 
e.g. cerebellum chopping.


On 
Wed, 28 Jun 2006 [EMAIL PROTECTED] wrote:



I am currently in the process of manual editing...just curious though,
what exatly does adding an atlas do to the skullstrip process?

Quoting Nick Schmansky [EMAIL PROTECTED]:


First have a look at the troubleshooting wiki pages at:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

In particular, Subject 1 has a skull strip problem, and the fix info
is
here:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix

I'm guessing you have seen this page since you have already
attempted
one type of fix (adjusting the watershed parameters).  The
alternative
fix is the slice-by-slice manual editing.

You could also try adding the wsatlas flag:

  recon-all -s (subject) -skullstrip -wsatlas

which will use an atlas to help with the skull-strip.

Does the contrast of your image look good?  That is, comparing your
orig.mgz to that of the sample subject 'bert' included with
freesurfer?

Nick


On Wed, 2006-06-28 at 10:09 -0400, [EMAIL PROTECTED] wrote:

I am having trouble with one of my skull strips, and getting very
extreme results.  When I re-run the skullstrip using different

watershed

values, anything at 56% or below takes 75%+ of the brain out, and

as

soon as I jump to 57% or higher, it leaves on almost all of the

skull,

except for maybe 5% of it.  Is this indicative of a more

complicated

problem, and what is my next step (other than manually taking off

the

skull), if any?
Thanks
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