Hi Clare, I just posted something you may want to try, detailing some flags/expert options that we tried that yielded dramatically better temporal lobe surfaces for us.

cheers, -MH

On Tue, 2012-01-10 at 15:38 +0000, Gibbard, Clare wrote:

Hi Bruce,

Thank you for your quick reply. I installed v5.1.0 from the website and that name is what comes up when I open a terminal window. However, I tried typing recon-all -version and got $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $. So I'm not sure if that means the version is different from what I thought.

I tried to upload 3 directories to the FTP in /transfer/incoming/claregibbard.tar. subject_1010_orig is the subject before adding control points. subject_1010_cpleft is after I added control points to the left temporal lobe. subject_1010_cpleftandright is when I tried adding control points to both the left and right temporal lobe. However, I can't tell if they have uploaded or not (it was taking a long time, but when I aborted the upload it said File receive OK). If you need me to, I can try sending you fewer files.

I hope that helps. Let me know if you need any more information.

Best wishes, Clare

---

From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 10 January 2012 13:40 To: Gibbard, Clare Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe cut off

Hi Claire,

hmmm, that is odd. What version are you running? If you upload the subject before and after we'll take a look Bruce On Tue, 10 Jan 2012, Gibbard, Clare wrote:

...

Hi,

I ran recon-all -all -subjid subjectx on around 40 scans. The registrations and skull strips look fine. However, the white matter and pial surface segmentations miss out the left anterior temporal lobe in most subjects. I tried adding in control points to the left temporal lobe and running recon-all -autorecon2-cp -autorecon3 -subjid subjectx. This helped to fill in the missing areas, but new parts of the right temporal lobe were cut out. I then tried adding in control points to both the left and right temporal lobes, but again new regions of the left temporal lobe were cut out. I think it must be an intensity issue, but I can't see how to fix it. Are you able to give me a work flow to sort this?

Here are some screenshots:

[moz-screenshot.png] [moz-screenshot-1.png] Before control points added:

[IMAGE]

After control points added to left and right temporal lobes:

[IMAGE]

Thank you.

Best wishes, Clare Gibbard

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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Clare,

I had that same error a few months ago. (I had the error in 1 out of 500+cases). Someone on the list had suggested the following solution:

"Alternatively you can try rerunning the skullstrip step, sometimes this works as well. recon-all -skullstrip -autorecon2 -autorecon3 -s [SubjID]"

This had worked for me. I guess you can add the expert options to the above command and see if it works for you. Good luck Mehul

On Thu, Jan 12, 2012 at 9:39 AM, Gibbard, Clare c.gibbard@ucl.ac.uk wrote:

Hi Bruce,

In order to solve the temporal lobe issue in my scans I ran recon-all again from scratch using an expert option to run the mri_normalize command with the -b 20 and -n5 options (as per Michael Harms' email to the mailing list): recon-all -all -subjid subject_1010 -expert /home/clare/freesurfer/subjects/subject_1010/scripts/expert.opts

It seemed to be running well, but exited early with the following error message: ERROR: _FindFacePath: could not find path!

I've seen that other people have had this problem, but can't see the solution. I have started uploading my subject to your file exchange (the clarefilepatherror.tar file), but it seems to be taking some time. Let me know if you don't get it. I've attached the log to this email if that helps as well. I would really appreciate some advice on fixing this. Thank you.

Best wishes, Clare

---

From: Gibbard, Clare Sent: 10 January 2012 15:38 To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu; Gibbard, Clare Subject: RE: [Freesurfer] temporal lobe cut off

Hi Bruce,

Thank you for your quick reply. I installed v5.1.0 from the website and that name is what comes up when I open a terminal window. However, I tried typing recon-all -version and got $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $. So I'm not sure if that means the version is different from what I thought.

I tried to upload 3 directories to the FTP in /transfer/incoming/claregibbard.tar. subject_1010_orig is the subject before adding control points. subject_1010_cpleft is after I added control points to the left temporal lobe. subject_1010_cpleftandright is when I tried adding control points to both the left and right temporal lobe. However, I can't tell if they have uploaded or not (it was taking a long time, but when I aborted the upload it said File receive OK). If you need me to, I can try sending you fewer files.

I hope that helps. Let me know if you need any more information.

Best wishes, Clare

---

From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 10 January 2012 13:40 To: Gibbard, Clare Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe cut off

Hi Claire,

hmmm, that is odd. What version are you running? If you upload the subject before and after we'll take a look Bruce On Tue, 10 Jan 2012, Gibbard, Clare wrote:

...

Hi,

I ran recon-all -all -subjid subjectx on around 40 scans. The

registrations and skull strips look fine. However, the white matter and pial surface segmentations

...

miss out the left anterior temporal lobe in most subjects. I tried

adding in control points to the left temporal lobe and running recon-all -autorecon2-cp

...

-autorecon3 -subjid subjectx. This helped to fill in the missing areas,

but new parts of the right temporal lobe were cut out. I then tried adding in control

...

points to both the left and right temporal lobes, but again new regions

of the left temporal lobe were cut out. I think it must be an intensity issue, but I can't

...

see how to fix it. Are you able to give me a work flow to sort this?

Here are some screenshots:

[moz-screenshot.png] [moz-screenshot-1.png] Before control points added:

[IMAGE]

After control points added to left and right temporal lobes:

[IMAGE]

Thank you.

Best wishes, Clare Gibbard

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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.