Hi Katie

I defer to others for this particular problem, but I would strongly advise looking at the various volumes recon-all outputted prior to that and make sure that they are all reasonable-looking. Can you also tell us what your input data is?

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Katherine Andrade
Sent: Monday, February 8, 2021 1:05 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Issue with Segmentation

        External Email - Use Caution        

Hi Bruce,

Thank you for your prompt  response. We were able to successfully run segmentation on another dataset that we've received from one University but when we attempt to run the segmentation from the dataset from another University, we can't complete segmentation. 

This is what Matlab says: 

---------------------------------------------------------------------------------------

Checking to see if freesurfer segmentation has started...
Freesurfer segmentation has started; this process may take more than 24 hours...
The progress of the segmentation process can be observed by opening /home/bdl/freesurfer/subjects/SD06/scripts/recon-all.log
When the segmentation is complete the results are saved in /home/bdl/freesurfer/subjects/SD06/...The pial surfaces are saved as rh.pial and lh.pial in SD06/surf/...

Segmentation processing... Please don't turn off your computer!

-----------------------------------------------------------------------------------------

I've attached the recon-all.log below and it mentions there is an Error that says "don't know how to get DWI parameters from.

Is there anyway you can help me debug this issue. I know this process shouldn't be taking so long.

Best,

Katie

On Sun, Feb 7, 2021 at 2:38 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

Hi Katie

Can you give us more info? What command line did you run? Can you send us the recon-all.log file from the subject so we can see what step it is on? Usually this means the topology fixer is trying to fix something giant, like the cerebellum attached to cortex or skull left around or something

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Katherine Andrade
Sent: Sunday, February 7, 2021 5:22 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue with Segmentation

        External Email - Use Caution        

To whom this may concern,

I've been running segmentation for over 100 hours and I'm  not entirely sure how to fix this issue. Is this the right address to ask for help?

Best,

Katie

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