Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

2020-01-31 Thread Bruce Fischl 

glad to hear it
Bruce
On Fri, 31 Jan 2020, Laurel Quinlan wrote:



External Email - Use Caution

Hi Bruce,

Thank you for your help! I removed the IsRunning.lh+rh script as well and
reran the recon. Everything seems to have worked!

-Laurel


From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Bruce Fischl

Sent: Tuesday, January 28, 2020 3:37 PM
To: Freesurfer support list 
Cc: Greve, Douglas N.,Ph.D. 
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
mri_relabel_hypointensities  
Hi Laurel

if a subject dir already exists recon-all will exit unless you specify
-force. Alternatively you can try using the -make all flag, which should
rerun only the steps that are needed (assuming the reboot didn't happen
e.g. in the middle of writing a file)

cheers
Bruce
On Tue, 28 Jan 2020, Laurel Quinlan
wrote:

>
> External Email - Use Caution
>
> Hi Doug,
>
> Thanks for looking over that file. It is the correct recon-all file for
one
> of the problem brains. I discovered that there was a system reboot of some
> sort when the recon-all was processing for these problem brains, so that
is
> likely what caused the process to stop. How can I restart the recon-all
> process for these brains? I have tried just rerunning the recon-all
command
> but the process exits within a few moments each time. I am wondering if
> there is something I need to delete that was partially processed during
the
> first attempt.
>
> Thanks,
>
> Laurel 
>
>___
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> Sent: Friday, January 24, 2020 9:34 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
> mri_relabel_hypointensities  
> It did not look like there was an explicit error in that log file, it just
> stops at mris_volmask. Is that the right recon-all? Also, please just send
> the text file so that we don't have to unzip it.
>
> On 1/22/2020 4:39 PM, Laurel Quinlan wrote:
>
>   External Email - Use Caution
>
> Hi FS Support,
>
> I have two brains for which recon-all exited with errors after I
> edited the wm.mgz volume. It seems that the problem occurs during the
> mri_segstats and mri_relabel_hypointensities steps (if I'm reading the
> output of the command "tail scripts/recon-all.log" correctly). I
> attached one of the recon-all.log files as a zipped txt file. Please
> let me know if you have troubleshooting suggestions.
>
> Thank you for your help!  
>
> Laurel Quinlan
> Research Specialist
> Center for Healthy Minds
> University of Wisconsin-Madison
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>

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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

2020-01-31 Thread Laurel Quinlan 
External Email - Use Caution

Hi Bruce,

Thank you for your help! I removed the IsRunning.lh+rh script as well and reran 
the recon. Everything seems to have worked!

-Laurel

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Tuesday, January 28, 2020 3:37 PM
To: Freesurfer support list 
Cc: Greve, Douglas N.,Ph.D. 
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and 
mri_relabel_hypointensities

Hi Laurel

if a subject dir already exists recon-all will exit unless you specify
-force. Alternatively you can try using the -make all flag, which should
rerun only the steps that are needed (assuming the reboot didn't happen
e.g. in the middle of writing a file)

cheers
Bruce
On Tue, 28 Jan 2020, Laurel Quinlan
wrote:

>
> External Email - Use Caution
>
> Hi Doug,
>
> Thanks for looking over that file. It is the correct recon-all file for one
> of the problem brains. I discovered that there was a system reboot of some
> sort when the recon-all was processing for these problem brains, so that is
> likely what caused the process to stop. How can I restart the recon-all
> process for these brains? I have tried just rerunning the recon-all command
> but the process exits within a few moments each time. I am wondering if
> there is something I need to delete that was partially processed during the
> first attempt.
>
> Thanks,
>
> Laurel
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> Sent: Friday, January 24, 2020 9:34 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
> mri_relabel_hypointensities
> It did not look like there was an explicit error in that log file, it just
> stops at mris_volmask. Is that the right recon-all? Also, please just send
> the text file so that we don't have to unzip it.
>
> On 1/22/2020 4:39 PM, Laurel Quinlan wrote:
>
>   External Email - Use Caution
>
> Hi FS Support,
>
> I have two brains for which recon-all exited with errors after I
> edited the wm.mgz volume. It seems that the problem occurs during the
> mri_segstats and mri_relabel_hypointensities steps (if I'm reading the
> output of the command "tail scripts/recon-all.log" correctly). I
> attached one of the recon-all.log files as a zipped txt file. Please
> let me know if you have troubleshooting suggestions.
>
> Thank you for your help!
>
> Laurel Quinlan
> Research Specialist
> Center for Healthy Minds
> University of Wisconsin-Madison
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

2020-01-28 Thread Bruce Fischl 

Hi Laurel

if a subject dir already exists recon-all will exit unless you specify 
-force. Alternatively you can try using the -make all flag, which should 
rerun only the steps that are needed (assuming the reboot didn't happen 
e.g. in the middle of writing a file)


cheers
Bruce
On Tue, 28 Jan 2020, Laurel Quinlan 
wrote:




External Email - Use Caution

Hi Doug,

Thanks for looking over that file. It is the correct recon-all file for one
of the problem brains. I discovered that there was a system reboot of some
sort when the recon-all was processing for these problem brains, so that is
likely what caused the process to stop. How can I restart the recon-all
process for these brains? I have tried just rerunning the recon-all command
but the process exits within a few moments each time. I am wondering if
there is something I need to delete that was partially processed during the
first attempt.

Thanks,

Laurel 


From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Greve, Douglas
N.,Ph.D. 
Sent: Friday, January 24, 2020 9:34 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
mri_relabel_hypointensities  
It did not look like there was an explicit error in that log file, it just
stops at mris_volmask. Is that the right recon-all? Also, please just send
the text file so that we don't have to unzip it.

On 1/22/2020 4:39 PM, Laurel Quinlan wrote:

  External Email - Use Caution

Hi FS Support,

I have two brains for which recon-all exited with errors after I
edited the wm.mgz volume. It seems that the problem occurs during the
mri_segstats and mri_relabel_hypointensities steps (if I'm reading the
output of the command "tail scripts/recon-all.log" correctly). I
attached one of the recon-all.log files as a zipped txt file. Please
let me know if you have troubleshooting suggestions.

Thank you for your help!  

Laurel Quinlan
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison


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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

2020-01-28 Thread Laurel Quinlan 
External Email - Use Caution

Hi Doug,

Thanks for looking over that file. It is the correct recon-all file for one of 
the problem brains. I discovered that there was a system reboot of some sort 
when the recon-all was processing for these problem brains, so that is likely 
what caused the process to stop. How can I restart the recon-all process for 
these brains? I have tried just rerunning the recon-all command but the process 
exits within a few moments each time. I am wondering if there is something I 
need to delete that was partially processed during the first attempt.

Thanks,

Laurel

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Friday, January 24, 2020 9:34 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and 
mri_relabel_hypointensities

It did not look like there was an explicit error in that log file, it just 
stops at mris_volmask. Is that the right recon-all? Also, please just send the 
text file so that we don't have to unzip it.

On 1/22/2020 4:39 PM, Laurel Quinlan wrote:

External Email - Use Caution

Hi FS Support,

I have two brains for which recon-all exited with errors after I edited the 
wm.mgz volume. It seems that the problem occurs during the mri_segstats and 
mri_relabel_hypointensities steps (if I'm reading the output of the command 
"tail scripts/recon-all.log" correctly). I attached one of the recon-all.log 
files as a zipped txt file. Please let me know if you have troubleshooting 
suggestions.

Thank you for your help!

Laurel Quinlan
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison




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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

2020-01-24 Thread Greve, Douglas N.,Ph.D. 
It did not look like there was an explicit error in that log file, it just 
stops at mris_volmask. Is that the right recon-all? Also, please just send the 
text file so that we don't have to unzip it.

On 1/22/2020 4:39 PM, Laurel Quinlan wrote:

External Email - Use Caution

Hi FS Support,

I have two brains for which recon-all exited with errors after I edited the 
wm.mgz volume. It seems that the problem occurs during the mri_segstats and 
mri_relabel_hypointensities steps (if I'm reading the output of the command 
"tail scripts/recon-all.log" correctly). I attached one of the recon-all.log 
files as a zipped txt file. Please let me know if you have troubleshooting 
suggestions.

Thank you for your help!

Laurel Quinlan
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison




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