Re: [Freesurfer] 001 vs brainmask views in freeview
Yes, these two volume are aligned. But they are sliced differently. When
you display a single volume alone in freeview, it is by default
displayed in its native slice orientation.
Ruopeng
On 9/16/19 3:39 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
I’m still a little confused. When I open up the brainmask.mgz in
freeview I see the following. It is rotated compared to the native
001.mgz below.
I then open the 001.mgz with freeview in a NEW terminal (seperate
session), I get the following. Should thy not be the same orientation?
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Ruopeng Wang
*Sent:* Monday, September 16, 2019 1:17 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] 001 vs brainmask views in freeview
The first volume is always displayed in its original orientation where
pixel data are stored. So that the pixel data don't get resampled
(unless you force it with '-r' flag to resample it in standard RAS).
Ruopeng
On 9/16/19 1:06 PM, Alexopoulos, Dimitrios wrote:
*External Email - Use Caution *
Thanks for info.
If I open only the brainmsk.mgz only from a new terminal it is
rotated and not in its native orientation (which is 001’s
orientation).
Why does it not appear to be in native space in freeview?
Jim
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of
*Ruopeng Wang
*Sent:* Monday, September 16, 2019 11:51 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] 001 vs brainmask views in freeview
Hi,
When you load brainmask.mgz as the second volume, it will be
realigned to 001.mgz. The default resample method is
nearest-neighbor. Thus you get the blocky look. You can try
loading it with trilinear or cubic resampling like this from the
command-line:
freeview -v 001.mgz brainmask.mgz -trilinear
Ruopeng
On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote:
*External Email - Use Caution *
Hi all,
I ran a 2yo subject through FS6.0 using ‘recon-all -i
/firstdicom.dcm -all’ and the output segmentations and
surfaces looks good.
Can someone explain why I see different alignments when I view
the 001.mgz and brainmask.mgz files in freeview, depending on
the order files are opened.
001.mgz AND brainmask.mgz -- 001 opened first in freeview
followed by brainmask.mgz. Alignemnts OK but brainmask looks
grainy.
Brainmask.mgz opened only in a new terminal. Rotated and looks
smoother than brainmask above.
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Re: [Freesurfer] 001 vs brainmask views in freeview
External Email - Use Caution I'm still a little confused. When I open up the brainmask.mgz in freeview I see the following. It is rotated compared to the native 001.mgz below. [cid:image002.jpg@01D56C9C.9A38CF50] I then open the 001.mgz with freeview in a NEW terminal (seperate session), I get the following. Should thy not be the same orientation? [cid:image007.jpg@01D56C9C.9A38CF50] From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ruopeng Wang Sent: Monday, September 16, 2019 1:17 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 001 vs brainmask views in freeview The first volume is always displayed in its original orientation where pixel data are stored. So that the pixel data don't get resampled (unless you force it with '-r' flag to resample it in standard RAS). Ruopeng On 9/16/19 1:06 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Thanks for info. If I open only the brainmsk.mgz only from a new terminal it is rotated and not in its native orientation (which is 001's orientation). Why does it not appear to be in native space in freeview? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Ruopeng Wang Sent: Monday, September 16, 2019 11:51 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] 001 vs brainmask views in freeview Hi, When you load brainmask.mgz as the second volume, it will be realigned to 001.mgz. The default resample method is nearest-neighbor. Thus you get the blocky look. You can try loading it with trilinear or cubic resampling like this from the command-line: freeview -v 001.mgz brainmask.mgz -trilinear Ruopeng On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, I ran a 2yo subject through FS6.0 using 'recon-all -i /firstdicom.dcm -all' and the output segmentations and surfaces looks good. Can someone explain why I see different alignments when I view the 001.mgz and brainmask.mgz files in freeview, depending on the order files are opened. 001.mgz AND brainmask.mgz -- 001 opened first in freeview followed by brainmask.mgz. Alignemnts OK but brainmask looks grainy. [cid:image001.jpg@01D56C9B.65CA38E0][cid:image003.jpg@01D56C9B.65CA38E0] Brainmask.mgz opened only in a new terminal. Rotated and looks smoother than brainmask above. [cid:image004.jpg@01D56C9B.65CA38E0] The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 001 vs brainmask views in freeview
The first volume is always displayed in its original orientation where pixel data are stored. So that the pixel data don't get resampled (unless you force it with '-r' flag to resample it in standard RAS). Ruopeng On 9/16/19 1:06 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Thanks for info. If I open only the brainmsk.mgz only from a new terminal it is rotated and not in its native orientation (which is 001’s orientation). Why does it not appear to be in native space in freeview? Jim *From:*freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Ruopeng Wang *Sent:* Monday, September 16, 2019 11:51 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] 001 vs brainmask views in freeview Hi, When you load brainmask.mgz as the second volume, it will be realigned to 001.mgz. The default resample method is nearest-neighbor. Thus you get the blocky look. You can try loading it with trilinear or cubic resampling like this from the command-line: freeview -v 001.mgz brainmask.mgz -trilinear Ruopeng On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote: *External Email - Use Caution * Hi all, I ran a 2yo subject through FS6.0 using ‘recon-all -i /firstdicom.dcm -all’ and the output segmentations and surfaces looks good. Can someone explain why I see different alignments when I view the 001.mgz and brainmask.mgz files in freeview, depending on the order files are opened. 001.mgz AND brainmask.mgz -- 001 opened first in freeview followed by brainmask.mgz. Alignemnts OK but brainmask looks grainy. Brainmask.mgz opened only in a new terminal. Rotated and looks smoother than brainmask above. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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
Re: [Freesurfer] 001 vs brainmask views in freeview
External Email - Use Caution Thanks for info. If I open only the brainmsk.mgz only from a new terminal it is rotated and not in its native orientation (which is 001's orientation). Why does it not appear to be in native space in freeview? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ruopeng Wang Sent: Monday, September 16, 2019 11:51 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 001 vs brainmask views in freeview Hi, When you load brainmask.mgz as the second volume, it will be realigned to 001.mgz. The default resample method is nearest-neighbor. Thus you get the blocky look. You can try loading it with trilinear or cubic resampling like this from the command-line: freeview -v 001.mgz brainmask.mgz -trilinear Ruopeng On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, I ran a 2yo subject through FS6.0 using 'recon-all -i /firstdicom.dcm -all' and the output segmentations and surfaces looks good. Can someone explain why I see different alignments when I view the 001.mgz and brainmask.mgz files in freeview, depending on the order files are opened. 001.mgz AND brainmask.mgz -- 001 opened first in freeview followed by brainmask.mgz. Alignemnts OK but brainmask looks grainy. [cid:image001.jpg@01D56C87.359CC930][cid:image002.jpg@01D56C87.359CC930] Brainmask.mgz opened only in a new terminal. Rotated and looks smoother than brainmask above. [cid:image003.jpg@01D56C87.359CC930] The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 001 vs brainmask views in freeview
Hi, When you load brainmask.mgz as the second volume, it will be realigned to 001.mgz. The default resample method is nearest-neighbor. Thus you get the blocky look. You can try loading it with trilinear or cubic resampling like this from the command-line: freeview -v 001.mgz brainmask.mgz -trilinear Ruopeng On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, I ran a 2yo subject through FS6.0 using ‘recon-all -i /firstdicom.dcm -all’ and the output segmentations and surfaces looks good. Can someone explain why I see different alignments when I view the 001.mgz and brainmask.mgz files in freeview, depending on the order files are opened. 001.mgz AND brainmask.mgz -- 001 opened first in freeview followed by brainmask.mgz. Alignemnts OK but brainmask looks grainy. Brainmask.mgz opened only in a new terminal. Rotated and looks smoother than brainmask above. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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
