External Email - Use Caution
Thank you for your reply.
Is it impossible with 2mm? Unfortunately, the data we collect for the study all have same thickness of voxel. And, there was a problem like the photo below, and only the recon-all.log could be attached to you.
Thanks, Jeongson ----------------------------------------------------------------------
Message: 1 Date: Thu, 20 Dec 2018 10:13:16 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047 (60827, 60826, 59444) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1812201012130.17732@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi Jeongson
it certainly looks like something went badly wrong. 2mm may be too thick - we typically recommend <=1.5mm for any voxel direction. Can you send us the recon-all.log? And maybe a snapshot of the volume with the lh.orig.nofix and rh.orig.nofix overlaid?
cheers Bruce
On Thu, 20 Dec 2018, ??? wrote:
External Email - Use CautionHello Freesurfer developers I'm starting using FS and I have a problem running recon-all. #recon-all -s /usr/local/freesurfer/subjects/20180108 -all I've attached the output to a ERROR image file.
We're doing on a GE scanner 3T, T1-FSPGR axial slices, 3D with a slice thickness of 2.0mm. freesurfer version : freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
Any help is greatly appreciated.
Thanks.
Jeongson
------------------------------
did you try to load it as a surface? If you want to upload the entire subject dir (tarred and gzipped) to our ftp site we will take a look. In the meantime you can also just post an image of the volume in 3 planes, that might help
cheers Bruce On Fri, 21 Dec 2018, 허정선 wrote:
External Email - Use CautionThank you for your reply.
Is it impossible with 2mm? Unfortunately, the data we collect for the study all have same thickness of voxel. And, there was a problem like the photo below, and only the recon-all.log could be attached to you.
Thanks, Jeongson
Message: 1 Date: Thu, 20 Dec 2018 10:13:16 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047 (60827, 60826, 59444) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1812201012130.17732@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi Jeongson
it certainly looks like something went badly wrong. 2mm may be too thick
- we typically recommend <=1.5mm for any voxel direction. Can you send us
the recon-all.log? And maybe a snapshot of the volume with the lh.orig.nofix and rh.orig.nofix overlaid?
cheers Bruce
On Thu, 20 Dec 2018, ??? wrote:
External Email - Use CautionHello Freesurfer developers I'm starting using FS and I have a problem running recon-all. #recon-all -s /usr/local/freesurfer/subjects/20180108 -all I've attached the output to a ERROR image file.
We're doing on a GE scanner 3T, T1-FSPGR axial slices, 3D with a slice thickness of 2.0mm. freesurfer version : freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
Any help is greatly appreciated.
Thanks.
Jeongson
Hi Jeongson,
I took a look at your data, thank you for uploading it. Your recon is likely failing because your case has a large pathology that is causing your white matter surface to be topologically incorrect. I recommend filling in that whole area on the wm.mgz mask and re-running the rest of your recon using the instructions on the page below.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0
Please let us know if you have questions, or if your recon still fails after these edits.
Best,
Emma
Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, December 21, 2018 12:13:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047
did you try to load it as a surface? If you want to upload the entire subject dir (tarred and gzipped) to our ftp site we will take a look. In the meantime you can also just post an image of the volume in 3 planes, that might help
cheers Bruce On Fri, 21 Dec 2018, 허정선 wrote:
External Email - Use CautionThank you for your reply.
Is it impossible with 2mm? Unfortunately, the data we collect for the study all have same thickness of voxel. And, there was a problem like the photo below, and only the recon-all.log could be attached to you.
Thanks, Jeongson
Message: 1 Date: Thu, 20 Dec 2018 10:13:16 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047 (60827, 60826, 59444) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1812201012130.17732@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi Jeongson
it certainly looks like something went badly wrong. 2mm may be too thick
- we typically recommend <=1.5mm for any voxel direction. Can you send us
the recon-all.log? And maybe a snapshot of the volume with the lh.orig.nofix and rh.orig.nofix overlaid?
cheers Bruce
On Thu, 20 Dec 2018, ??? wrote:
External Email - Use CautionHello Freesurfer developers I'm starting using FS and I have a problem running recon-all. #recon-all -s /usr/local/freesurfer/subjects/20180108 -all I've attached the output to a ERROR image file.
We're doing on a GE scanner 3T, T1-FSPGR axial slices, 3D with a slice thickness of 2.0mm. freesurfer version : freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
Any help is greatly appreciated.
Thanks.
Jeongson
freesurfer@nmr.mgh.harvard.edu
-
Boyd, Emma -
Bruce Fischl -
허정선