External Email - Use Caution
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 mailto: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:
External Email - Use CautionHi 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 mailto: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:
External Email - Use CautionHello 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Dengyu
if you want to upload volumes use our ftp server
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers Bruce On Wed, 8 May 2019, Dengyu Wang wrote:
External Email - Use CautionHi 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 mailto: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:
External Email - Use CautionHi 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 mailto: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:
External Email - Use CautionHello 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce, I have uploaded wm.mgz, lh.orig.nofix, and rh.orig.nofix to transfer/incoming/. Thank you!
Best, Dengyu
On May 8, 2019, at 11:46 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dengyu
if you want to upload volumes use our ftp server
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers Bruce On Wed, 8 May 2019, Dengyu Wang wrote:
External Email - Use CautionHi 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 mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto: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:
External Email - Use Caution 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 mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto: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:
> External Email - Use Caution > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Dengyu
can you upload the entire tarred and gzipped subject dir instead?
thanks Bruce On Wed, 8 May 2019, Dengyu Wang wrote:
External Email - Use Caution
Hi Bruce,I have uploaded wm.mgz, lh.orig.nofix, and rh.orig.nofix to transfer/incoming/. Thank you!
Best, Dengyu
On May 8, 2019, at 11:46 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:Hi Dengyu
if you want to upload volumes use our ftp server
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers Bruce On Wed, 8 May 2019, Dengyu Wang wrote:
External Email - Use Caution 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 <mailto: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: External Email - Use Caution 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 <mailto: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: External Email - Use Caution 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce, Sure! I have uploaded the tarred and gzipped folder of the subject to the transfer/incoming folder.
Thank you!
Best, Dengyu
On May 8, 2019, at 1:32 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dengyu
can you upload the entire tarred and gzipped subject dir instead?
thanks Bruce On Wed, 8 May 2019, Dengyu Wang wrote:
External Email - Use CautionHi Bruce,I have uploaded wm.mgz, lh.orig.nofix, and rh.orig.nofix to transfer/incoming/. Thank you! Best, Dengyu
On May 8, 2019, at 11:46 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:Hi Dengyu if you want to upload volumes use our ftp server https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange cheers Bruce On Wed, 8 May 2019, Dengyu Wang wrote:
External Email - Use Caution 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 <mailto: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: External Email - Use Caution 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 <mailto: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: External Email - Use Caution 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Dengyu Wang -
Dengyu Wang