________________________________ From: Paul, Rahul Sent: Thursday, January 28, 2021 3:52 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer recon all
Hi,
I just started working on the freesurfer software. I was trying to use recon-all command but there was an output saying XL error detected, and it remained same for more than 6 hours or so.
Any idea how I can fix it? Bdw i stopped it running after 8 hours or so.
I am using a T1-MRI scan. I am using a MacBook pro (8GB RAM). I am attaching a screenshot and the command I used can be seen in the bottom of the screenshot.
Thank you,
Rahul Paul
Hi Rahul
That typically means that something has gone wrong, like too much skull being left around. The timing of the defect correction is quadratic in the size of the largest defect, so quite fast for small ones, but very very slow for big ones (and less likely to be correct when done). Look at the inflated.nofix surface and the wm.mgz and see if you can understand why this is happening. There is also a label file that gets generated for the defects that you can load and use to visualize them.
Also, please don't send snapshots of text - just embed the text in the email so we can search and copy and paste and such Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Paul, Rahul Sent: Friday, January 29, 2021 12:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fw: Freesurfer recon all
________________________________ From: Paul, Rahul Sent: Thursday, January 28, 2021 3:52 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Freesurfer recon all
Hi,
I just started working on the freesurfer software. I was trying to use recon-all command but there was an output saying XL error detected, and it remained same for more than 6 hours or so.
Any idea how I can fix it? Bdw i stopped it running after 8 hours or so.
I am using a T1-MRI scan. I am using a MacBook pro (8GB RAM). I am attaching a screenshot and the command I used can be seen in the bottom of the screenshot.
Thank you,
Rahul Paul
Hi Bruce,
Is it possible to do a zoom call for troubleshooting with me and my PI today?
Rahul ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu Sent: Friday, January 29, 2021 12:35 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer recon all
Hi Rahul
That typically means that something has gone wrong, like too much skull being left around. The timing of the defect correction is quadratic in the size of the largest defect, so quite fast for small ones, but very very slow for big ones (and less likely to be correct when done). Look at the inflated.nofix surface and the wm.mgz and see if you can understand why this is happening. There is also a label file that gets generated for the defects that you can load and use to visualize them.
Also, please don’t send snapshots of text – just embed the text in the email so we can search and copy and paste and such
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Paul, Rahul Sent: Friday, January 29, 2021 12:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fw: Freesurfer recon all
________________________________
From: Paul, Rahul Sent: Thursday, January 28, 2021 3:52 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Freesurfer recon all
Hi,
I just started working on the freesurfer software. I was trying to use recon-all command but there was an output saying XL error detected, and it remained same for more than 6 hours or so.
Any idea how I can fix it? Bdw i stopped it running after 8 hours or so.
I am using a T1-MRI scan. I am using a MacBook pro (8GB RAM). I am attaching a screenshot and the command I used can be seen in the bottom of the screenshot.
Thank you,
Rahul Paul
Hi Rahul
No, sorry, I cannot. Can you post some pictures of the wm.mgz? And/or the inflated.nofix?
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Paul, Rahul Sent: Friday, January 29, 2021 4:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer recon all
Hi Bruce,
Is it possible to do a zoom call for troubleshooting with me and my PI today?
Rahul ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, January 29, 2021 12:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer recon all
Hi Rahul
That typically means that something has gone wrong, like too much skull being left around. The timing of the defect correction is quadratic in the size of the largest defect, so quite fast for small ones, but very very slow for big ones (and less likely to be correct when done). Look at the inflated.nofix surface and the wm.mgz and see if you can understand why this is happening. There is also a label file that gets generated for the defects that you can load and use to visualize them.
Also, please don't send snapshots of text - just embed the text in the email so we can search and copy and paste and such
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Paul, Rahul Sent: Friday, January 29, 2021 12:24 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fw: Freesurfer recon all
________________________________
From: Paul, Rahul Sent: Thursday, January 28, 2021 3:52 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Freesurfer recon all
Hi,
I just started working on the freesurfer software. I was trying to use recon-all command but there was an output saying XL error detected, and it remained same for more than 6 hours or so.
Any idea how I can fix it? Bdw i stopped it running after 8 hours or so.
I am using a T1-MRI scan. I am using a MacBook pro (8GB RAM). I am attaching a screenshot and the command I used can be seen in the bottom of the screenshot.
Thank you,
Rahul Paul
You'll have to find and remove the defect manually. It is probably cerebellum that is still attached or maybe a piece of dura or skull. There is some info on defects here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freevi...
You can also run defect2seg --s subject should only take a few minutes Then run tkmeditfv subject brain.finalsurfs.mgz -defect -aux wm.mgz This will load the defects as a segmentation; there will also be a point set that you can use to go from one defect to another
On 1/29/2021 12:24 PM, Paul, Rahul wrote:
*From:* Paul, Rahul *Sent:* Thursday, January 28, 2021 3:52 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Freesurfer recon all Hi,
I just started working on the freesurfer software. I was trying to use recon-all command but there was an output saying XL error detected, and it remained same for more than 6 hours or so.
Any idea how I can fix it? Bdw i stopped it running after 8 hours or so.
I am using a T1-MRI scan. I am using a MacBook pro (8GB RAM). I am attaching a screenshot and the command I used can be seen in the bottom of the screenshot.
Thank you,
Rahul Paul
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