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Hello,
We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (https://secure-web.cisco.com/1acx6rTd53-Vz7knc_wTrpqifC8PTuiKKanQydzd8QVOyXk...).
The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output?
We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results.
Many thanks, Viki
External Email - Use Caution
Hello,
We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (FsTutorial/Talairach_freeview).
The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output?
We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results.
Many thanks, Viki
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tkregister2 is pretty old at this point; try using tkregsiterfv with the same option.
On 7/20/2023 7:06 PM, Viktorija Pratuseviciute wrote:
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Hello,
We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (FsTutorial/Talairach_freeview).
The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output?
We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results.
Many thanks,
Viki
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1RvLC4lcks9K_CvQkGcgn9YBtmNsMDbRRyS8vhwkZt8FQlG...
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Thank you very much! We did try the command tkregisterfv --s PI163 –fstal, however the recon-all processing fails before a surf/lh.white file is created and therefore an error is produced that this file can’t be found. Seems like with tkregisterfv the default is for it to require the lh.white file?
Many thanks,
Viki
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Date: Friday, July 21, 2023 at 6:28 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tkregister2 GUI not responding fully
External Email - Use Caution tkregister2 is pretty old at this point; try using tkregsiterfv with the same option. On 7/20/2023 7:06 PM, Viktorija Pratuseviciute wrote:
External Email - Use Caution Hello,
We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (FsTutorial/Talairach_freeview).
The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output?
We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results.
Many thanks, Viki
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Try adding --no-surfs
On 7/24/2023 12:45 PM, Viktorija Pratuseviciute wrote:
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Thank you very much! We did try the command tkregisterfv --s PI163 –fstal, however the recon-all processing fails before a surf/lh.white file is created and therefore an error is produced that this file can’t be found. Seems like with tkregisterfv the default is for it to require the lh.white file?
Many thanks,
Viki
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Friday, July 21, 2023 at 6:28 AM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Tkregister2 GUI not responding fully
* External Email - Use Caution *
tkregister2 is pretty old at this point; try using tkregsiterfv with the same option.
On 7/20/2023 7:06 PM, Viktorija Pratuseviciute wrote:
* External Email - Use Caution * Hello, We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (FsTutorial/Talairach_freeview). The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output? We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results. Many thanks, Viki _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/120PqAOhYldrRrLIEevPVe3qHhq_ir5ey6gQy-1IlNTowbI6kI9RiR3mD-h-DQgD5KCvR_PuGkpvOMQJOQ0ilNIYSNyLHR_EW5t3PRaH21YVii0o_kF5ZLyW_u2WKpejG-2GuZzvgB5GvFxVuG2L5BxRtyf8nZV_90M3ADSCGGsDcTIzvaTKqRn3XO2YiZvGKIYNf72dck2TvjM7n146i8Eem2vkJg1LSaLiVHUwXR_e8pAo8lP59p0mH0VcrIOFG/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1RvLC4lcks9K_CvQkGcgn9YBtmNsMDbRRyS8vhwkZt8FQlGeWR2YFrtTslWp5S7mjaO6f-4HXhZtvYnrBlBCAOrVgHW0EAjugB1tX8Y80CFI2aJhtapDr1DjFQHZeH40D9VQptjv8WNnZoIwy0oBCANbVrNzPgJb0MdoIAtBAtAzlPGDiRiqBgxkT6E9mUAcLimZ4Gmnd9Yls-bpvzo2-ziIZX8DR0RCAZrXXv8VL5BOniqjJxtW0YmnhqwE8wmKMd4cL8kJjwkhvYFu-UOxWxA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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I tried adding the –no-surfs (e.g. tkregisterfv --s PI163_noflair --no-surfs), however receive the below error message: ERROR: must spec a moveable volume
Many thanks,
Viki
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Date: Monday, July 31, 2023 at 3:39 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tkregister2 GUI not responding fully
External Email - Use Caution Try adding --no-surfs On 7/24/2023 12:45 PM, Viktorija Pratuseviciute wrote:
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Thank you very much! We did try the command tkregisterfv --s PI163 –fstal, however the recon-all processing fails before a surf/lh.white file is created and therefore an error is produced that this file can’t be found. Seems like with tkregisterfv the default is for it to require the lh.white file?
Many thanks,
Viki
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Friday, July 21, 2023 at 6:28 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tkregister2 GUI not responding fully
External Email - Use Caution tkregister2 is pretty old at this point; try using tkregsiterfv with the same option. On 7/20/2023 7:06 PM, Viktorija Pratuseviciute wrote:
External Email - Use Caution Hello,
We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (FsTutorial/Talairach_freeview).
The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output?
We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results.
Many thanks, Viki
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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what are you trying to do? This is for viewing the registration between two volumes. One of the volumes is obtained from the subject, but you need to specify the other volume on the command line (eg, --mov fmri.nii.gz)
On 10/3/2023 3:18 PM, Viktorija Pratuseviciute wrote:
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I tried adding the –no-surfs (e.g. tkregisterfv --s PI163_noflair --no-surfs),however receive the below error message:
ERROR: must spec a moveable volume
Many thanks,
Viki
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Monday, July 31, 2023 at 3:39 PM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Tkregister2 GUI not responding fully
* External Email - Use Caution *
Try adding --no-surfs
On 7/24/2023 12:45 PM, Viktorija Pratuseviciute wrote:
* External Email - Use Caution * Thank you very much! We did try the command tkregisterfv --s PI163 –fstal, however the recon-all processing fails before a surf/lh.white file is created and therefore an error is produced that this file can’t be found. Seems like with tkregisterfv the default is for it to require the lh.white file? Many thanks, Viki *From: *freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Date: *Friday, July 21, 2023 at 6:28 AM *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Tkregister2 GUI not responding fully * External Email - Use Caution * tkregister2 is pretty old at this point; try using tkregsiterfv with the same option. On 7/20/2023 7:06 PM, Viktorija Pratuseviciute wrote: * External Email - Use Caution * Hello, We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (FsTutorial/Talairach_freeview). The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output? We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results. Many thanks, Viki _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1RvLC4lcks9K_CvQkGcgn9YBtmNsMDbRRyS8vhwkZt8FQlGeWR2YFrtTslWp5S7mjaO6f-4HXhZtvYnrBlBCAOrVgHW0EAjugB1tX8Y80CFI2aJhtapDr1DjFQHZeH40D9VQptjv8WNnZoIwy0oBCANbVrNzPgJb0MdoIAtBAtAzlPGDiRiqBgxkT6E9mUAcLimZ4Gmnd9Yls-bpvzo2-ziIZX8DR0RCAZrXXv8VL5BOniqjJxtW0YmnhqwE8wmKMd4cL8kJjwkhvYFu-UOxWxA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/120PqAOhYldrRrLIEevPVe3qHhq_ir5ey6gQy-1IlNTowbI6kI9RiR3mD-h-DQgD5KCvR_PuGkpvOMQJOQ0ilNIYSNyLHR_EW5t3PRaH21YVii0o_kF5ZLyW_u2WKpejG-2GuZzvgB5GvFxVuG2L5BxRtyf8nZV_90M3ADSCGGsDcTIzvaTKqRn3XO2YiZvGKIYNf72dck2TvjM7n146i8Eem2vkJg1LSaLiVHUwXR_e8pAo8lP59p0mH0VcrIOFG/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Viktorija Pratuseviciute