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Hi all!
We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with:
tkregister2 --mgz --s <subject> --fstal --surf orig
and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference).
What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead?
Attached you will find example tkregister2 output screenshots.
Best regards, Agnieszka Sabisz
If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skull stripping?
On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:
External Email - Use Caution
Hi all!
We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with:
tkregister2 --mgz --s <subject> --fstal --surf orig
and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference).
What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead?
Attached you will find example tkregister2 output screenshots.
Best regards, Agnieszka Sabisz
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Doug, I checked skull stripping and I think it's all right. (see in attachment) The registration looks all right in translational directions but not in scaling. In the attachment you can see the comparison between tkregister view and freeview of the same patient. What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Best regards, Agnieszka
sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu napisał(a):
If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skull stripping?
On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:
External Email - Use CautionHi all!
We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with:
tkregister2 --mgz --s <subject> --fstal --surf orig
and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference).
What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead?
Attached you will find example tkregister2 output screenshots.
Best regards, Agnieszka Sabisz
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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Dear Freesurfer Team, I checked skull stripping and I think it's all right. (see in attachment) The registration looks all right in translational directions but not in scaling. In the attachment you can see the comparison between tkregister view and freeview of the same patient. What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Best regards, Agnieszka
sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu napisał(a):
If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skull stripping?
On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:
External Email - Use CautionHi all!
We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with:
tkregister2 --mgz --s <subject> --fstal --surf orig
and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference).
What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead?
Attached you will find example tkregister2 output screenshots.
Best regards, Agnieszka Sabisz
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
That is a little strange. Can you tar up the data and upload it to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/24/19 4:53 AM, Agnieszka Sabisz wrote:
External Email - Use Caution
Dear Freesurfer Team, I checked skull stripping and I think it's all right. (see in attachment) The registration looks all right in translational directions but not in scaling. In the attachment you can see the comparison between tkregister view and freeview of the same patient. What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Best regards, Agnieszka
sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> napisał(a):
If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skull stripping? On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with: tkregister2 --mgz --s <subject> --fstal --surf orig and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference). What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Attached you will find example tkregister2 output screenshots. Best regards, Agnieszka Sabisz _______________________________________________ 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
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Dear Doug, I uploaded the data by ftp in Windows 10. I hope You can see a tar file. The file's name is HTN_Con_096 and it contains the subject's folder after recon_all. Do You need any other data? All the best Agnieszka
pon., 29 lip 2019 o 22:44 Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu napisał(a):
That is a little strange. Can you tar up the data and upload it to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/24/19 4:53 AM, Agnieszka Sabisz wrote:
External Email - Use CautionDear Freesurfer Team, I checked skull stripping and I think it's all right. (see in attachment) The registration looks all right in translational directions but not in scaling. In the attachment you can see the comparison between tkregister view and freeview of the same patient. What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Best regards, Agnieszka
sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> napisał(a):
If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skull stripping? On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with: tkregister2 --mgz --s <subject> --fstal --surf orig and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference). What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Attached you will find example tkregister2 output screenshots. Best regards, Agnieszka Sabisz _______________________________________________ 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
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Dear Doug, I uploaded the data by ftp in Windows 10 on 1st Aug. I hope You can see a tar file. The file's name is HTN_Con_096 and it contains the subject's folder after recon_all. Do You need any other data? All the best
czw., 1 sie 2019 o 11:44 Agnieszka Sabisz agnieszkasabisz@gmail.com napisał(a):
Dear Doug, I uploaded the data by ftp in Windows 10. I hope You can see a tar file. The file's name is HTN_Con_096 and it contains the subject's folder after recon_all. Do You need any other data? All the best Agnieszka
pon., 29 lip 2019 o 22:44 Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu napisał(a):
That is a little strange. Can you tar up the data and upload it to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/24/19 4:53 AM, Agnieszka Sabisz wrote:
External Email - Use CautionDear Freesurfer Team, I checked skull stripping and I think it's all right. (see in
attachment)
The registration looks all right in translational directions but not in scaling. In the attachment you can see the comparison between tkregister view and freeview of the same patient. What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Best regards, Agnieszka
sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> napisał(a):
If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skullstripping?
On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with: tkregister2 --mgz --s <subject> --fstal --surf orig and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference). What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Attached you will find example tkregister2 output screenshots. Best regards, Agnieszka Sabisz _______________________________________________ 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
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Hi Agnieska, sorry for the delay. It looks like the contrast is slightly different than FS expects. I ran it with the -3T flag (which changes the talairach atlas), and it seemed to run fine on that subject. Try it out. best doug
On 8/19/2019 1:23 AM, Agnieszka Sabisz wrote:
External Email - Use Caution
Dear Doug, I uploaded the data by ftp in Windows 10 on 1st Aug. I hope You can see a tar file. The file's name is HTN_Con_096 and it contains the subject's folder after recon_all. Do You need any other data? All the best
czw., 1 sie 2019 o 11:44 Agnieszka Sabisz <agnieszkasabisz@gmail.commailto:agnieszkasabisz@gmail.com> napisał(a): Dear Doug, I uploaded the data by ftp in Windows 10. I hope You can see a tar file. The file's name is HTN_Con_096 and it contains the subject's folder after recon_all. Do You need any other data? All the best Agnieszka
pon., 29 lip 2019 o 22:44 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> napisał(a): That is a little strange. Can you tar up the data and upload it to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/24/19 4:53 AM, Agnieszka Sabisz wrote:
External Email - Use CautionDear Freesurfer Team, I checked skull stripping and I think it's all right. (see in attachment) The registration looks all right in translational directions but not in scaling. In the attachment you can see the comparison between tkregister view and freeview of the same patient. What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Best regards, Agnieszka
sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> napisał(a):
If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skull stripping? On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with: tkregister2 --mgz --s <subject> --fstal --surf orig and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference). What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Attached you will find example tkregister2 output screenshots. Best regards, Agnieszka Sabisz _______________________________________________ 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_______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Doug, Thanks a lot!!! 3t flag helps very much. The data looks fine now. All the best Agnieszka
pon., 19 sie 2019 o 15:59 Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu napisał(a):
Hi Agnieska, sorry for the delay. It looks like the contrast is slightly different than FS expects. I ran it with the -3T flag (which changes the talairach atlas), and it seemed to run fine on that subject. Try it out. best doug
On 8/19/2019 1:23 AM, Agnieszka Sabisz wrote:
External Email - Use CautionDear Doug, I uploaded the data by ftp in Windows 10 on 1st Aug. I hope You can see a tar file. The file's name is HTN_Con_096 and it contains the subject's folder after recon_all. Do You need any other data? All the best
czw., 1 sie 2019 o 11:44 Agnieszka Sabisz agnieszkasabisz@gmail.com napisał(a):
Dear Doug, I uploaded the data by ftp in Windows 10. I hope You can see a tar file. The file's name is HTN_Con_096 and it contains the subject's folder after recon_all. Do You need any other data? All the best Agnieszka
pon., 29 lip 2019 o 22:44 Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu napisał(a):
That is a little strange. Can you tar up the data and upload it to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/24/19 4:53 AM, Agnieszka Sabisz wrote:
External Email - Use CautionDear Freesurfer Team, I checked skull stripping and I think it's all right. (see in
attachment)
The registration looks all right in translational directions but not in scaling. In the attachment you can see the comparison between tkregister view and freeview of the same patient. What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Best regards, Agnieszka
sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> napisał(a):
If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skullstripping?
On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with: tkregister2 --mgz --s <subject> --fstal --surf orig and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference). What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Attached you will find example tkregister2 output screenshots. Best regards, Agnieszka Sabisz _______________________________________________ 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
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Agnieszka Sabisz -
Greve, Douglas N.,Ph.D.