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Hi Bruce,
My previous email with the wm.mgz and orig.nofix files was held by the system because of the big size. So in this email I attached some pictures about the wm and orig.nofix visualized in Freeview:

Hope to get your opinion. Thank you!

Best,
Dengyu

On May 8, 2019, at 11:01 AM, Dengyu Wang <wangdy1995@gmail.com> wrote:

Hi Bruce,
Thank you for your remind and I will keep in mind in the future.

Here are the wm.mgz, lh.orig.nofix and rh.orig.nofix

<wm.mgz>
<lh.orig.nofix>
<rh.orig.nofix>

I tried to open in Freeview but Freeview always collapsed.

Best,
Dengyu

On May 8, 2019, at 10:45 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Dengyu

I meant images of the brain. In general don't send us images of text - just send us the text so we can search and paste and such. In this case you have a huge defect that is probably caused by dura connecting to the wm. You need to look at the orig.nofix surfaces and the wm.mgz. You might need to make the skull stripping more aggressive and/or manually edit out some of the dura, but I can't tell without seeing the dataset.

cheers
Bruce
On Wed, 8 May 2019, Dengyu Wang wrote:

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Hi Bruce,
Thank you for your reply! And here is the detail:

I use the command below to start the reconstruction:



366 defects are found in the process:



And then says 281 defects to be corrected, and starts correcting the defect:


And then it gets stuck in correcting defect 46 and can’t move on:


We won’t have problem with t1 image without contrast, but in this special case we only have t1 with contrast. Do you have any ideas about this problem? Thank you!

Best,
Dengyu



On May 7, 2019, at 4:37 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Dengyu
you need to tell us what went wrong. We have reconned lots of brains with contrast, although sometimes the skull stripping needs to be played with to get it to work
cheers
Bruce
On Tue, 7 May 2019, Dengyu Wang wrote:

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Hello FreeSurfer developers,
I am writing to ask about problem I met when reconstructing cortex from MRI with contrast? I had one subject that had only with contrast MRI images, and the recon-all can’t finish successfully. Is there any method or parameter setting that can solve the problem? Thank you!
Best,
Dengyu
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