sure, our ftp site Bruce On Thu, 14 Dec 2017, Trevor K Day wrote:

Hi Bruce,

My apologies, I had forgotten that we had set FREESURFER_HOME up in our pipelines separately, and had I just got the version off of my shell.

We are using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Should I upload the subject somewhere?

Thanks,

Trevor

From: Bruce Fischl Sent: Thursday, December 14, 2017 7:06 AM To: Freesurfer support list Subject: Re: [Freesurfer] White/pial surface failure

Hi Trevor

would you consider moving to V6? The high res stream is *much* better in it than 5.3. If you can't, upload the subject and we will take a look

cheers Bruce

On Thu, 14 Dec 2017, Trevor K Day wrote:

...

Hello,

We are trying to run the high-resolution pipeline and it has failed spectacularly on one of our subjects.

Two images from recon_checker are attached.

I’m stumped because the command exits with an exit code of 0 and, in looking at the log, there no obvious indication of any error.

I’m not sure what to search because I don’t have an error message.

Recon-all.log is attached.

The brainmask is fine. Not perfect, but certainly not poor enough to cause this.

The intensity values of the T1 are perfectly normal, and there’s a bit of a motion artifact in the frontal lobe, but nothing that freesurfer hasn’t handled before.

Others have suggested that this seems to extreme to fix with control points, are the other approaches to take?

The command used was:

/usr/local/freesurfer/stable6_0/bin/recon-all \

-all -s 170661.s1 -hires -cw256 -qcache \

-i /mnt/panuc/udallp2/subjects/170661/session1/mprage/T1_256.nii.gz \

-expert /mnt/panuc/udallp2/lib/expert.opts

(Again, T1_256.nii.gz looks totally fine.)

The contents of expert.opts are mris_inflate -n 30

*  Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0   *  Platform: Debian GNU/Linux 8.9 (jessie)   *  Uname -a: Linux panuc 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2+deb8u5 (2017-09-19) x86_64      GNU/Linux

Where can I start to debug and fix this?

Thanks,

Trevor Day

Hi Trevor

we need the whole subject dir tarred and gzipped.

cheers Bruce

On Thu, 14 Dec 2017, Trevor K Day wrote:

Thanks, uploaded as 170661-T1_256.nii.gz

Trevor

From: Bruce Fischl Sent: Thursday, December 14, 2017 11:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] White/pial surface failure

sure, our ftp site Bruce On Thu, 14 Dec 2017, Trevor K Day wrote:

...

Hi Bruce,

My apologies, I had forgotten that we had set FREESURFER_HOME up in our pipelines separately, and had I just got the version off of my shell.

We are using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Should I upload the subject somewhere?

Thanks,

Trevor

From: Bruce Fischl Sent: Thursday, December 14, 2017 7:06 AM To: Freesurfer support list Subject: Re: [Freesurfer] White/pial surface failure

Hi Trevor

would you consider moving to V6? The high res stream is *much* better in it than 5.3. If you can't, upload the subject and we will take a look

cheers Bruce

On Thu, 14 Dec 2017, Trevor K Day wrote:

...

Hello,

We are trying to run the high-resolution pipeline and it has failed spectacularly on one of our subjects.

Two images from recon_checker are attached.

I’m stumped because the command exits with an exit code of 0 and, in looking at the log, there

no

...

...

obvious indication of any error.

I’m not sure what to search because I don’t have an error message.

Recon-all.log is attached.

The brainmask is fine. Not perfect, but certainly not poor enough to cause this.

The intensity values of the T1 are perfectly normal, and there’s a bit of a motion artifact in

the

...

...

frontal lobe, but nothing that freesurfer hasn’t handled before.

Others have suggested that this seems to extreme to fix with control points, are the other approaches to take?

The command used was:

/usr/local/freesurfer/stable6_0/bin/recon-all \

-all -s 170661.s1 -hires -cw256 -qcache \

-i /mnt/panuc/udallp2/subjects/170661/session1/mprage/T1_256.nii.gz \

-expert /mnt/panuc/udallp2/lib/expert.opts

(Again, T1_256.nii.gz looks totally fine.)

The contents of expert.opts are mris_inflate -n 30

*  Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0   *  Platform: Debian GNU/Linux 8.9 (jessie)   *  Uname -a: Linux panuc 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2+deb8u5 (2017-09-19) x86_64      GNU/Linux

Where can I start to debug and fix this?

Thanks,

Trevor Day

Hi,

Just wanted to follow up on this and see if anyone had a chance to look at it.

Thanks, Trevor

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________________________________ From: Trevor K Day Sent: Thursday, December 14, 2017 4:09:44 PM To: Freesurfer support list Subject: RE: [Freesurfer] White/pial surface failure

Gotcha, uploaded

From: Bruce Fischlmailto:fischl@nmr.mgh.harvard.edu Sent: Thursday, December 14, 2017 3:39 PM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White/pial surface failure

Hi Trevor

we need the whole subject dir tarred and gzipped.

cheers Bruce

On Thu, 14 Dec 2017, Trevor K Day wrote:

Thanks, uploaded as 170661-T1_256.nii.gz

Trevor

From: Bruce Fischl Sent: Thursday, December 14, 2017 11:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] White/pial surface failure

sure, our ftp site Bruce On Thu, 14 Dec 2017, Trevor K Day wrote:

...

Hi Bruce,

My apologies, I had forgotten that we had set FREESURFER_HOME up in our pipelines separately, and had I just got the version off of my shell.

We are using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Should I upload the subject somewhere?

Thanks,

Trevor

From: Bruce Fischl Sent: Thursday, December 14, 2017 7:06 AM To: Freesurfer support list Subject: Re: [Freesurfer] White/pial surface failure

Hi Trevor

would you consider moving to V6? The high res stream is *much* better in it than 5.3. If you can't, upload the subject and we will take a look

cheers Bruce

On Thu, 14 Dec 2017, Trevor K Day wrote:

...

Hello,

We are trying to run the high-resolution pipeline and it has failed spectacularly on one of our subjects.

Two images from recon_checker are attached.

I’m stumped because the command exits with an exit code of 0 and, in looking at the log, there

no

...

...

obvious indication of any error.

I’m not sure what to search because I don’t have an error message.

Recon-all.log is attached.

The brainmask is fine. Not perfect, but certainly not poor enough to cause this.

The intensity values of the T1 are perfectly normal, and there’s a bit of a motion artifact in

the

...

...

frontal lobe, but nothing that freesurfer hasn’t handled before.

Others have suggested that this seems to extreme to fix with control points, are the other approaches to take?

The command used was:

/usr/local/freesurfer/stable6_0/bin/recon-all \

            -all -s 170661.s1 -hires -cw256 -qcache \

            -i /mnt/panuc/udallp2/subjects/170661/session1/mprage/T1_256.nii.gz \

            -expert /mnt/panuc/udallp2/lib/expert.opts

(Again, T1_256.nii.gz looks totally fine.)

The contents of expert.opts are mris_inflate -n 30

• Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
• Platform: Debian GNU/Linux 8.9 (jessie)
• Uname -a: Linux panuc 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2+deb8u5 (2017-09-19) x86_64 GNU/Linux

Where can I start to debug and fix this?

Thanks,

Trevor Day