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Dear all,
I tried to check the talairach transformation under Freesurfer 7 linux version (freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551). However, neither command works as expected.
the command "freeview -v bert/mri/T1.mgz -v bert/mri/brainmask.mgz:reg=bert/mri/transforms/talairach.xfm" gives the following message in the terminal: "Not reading in xfm fileinfo". Both T1 and brainmask is loaded, but the transformation seems to be not applied.
the command "tkregisterfv --s bert --fstal --surf orig" works only without the flag --surf.
the command "tkregister2 --s bert --fstal" gives the following messages:
Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary"
The green border is not shown, only the target and movable images are visible.
Any idea how to fix this? Best, Gabor
External Email - Use Caution
I try to describe in more detail my problems with talairach check/correction in Freesurfer 7. In earlier versions, I used tkregister2 to check and correct talairach registration and it worked perfectly. The green line (orig surface of the subject) was very helpful in both checking and correcting the transformation. I can run tkregister2 under Freesurfer7 as well, but most of the buttons (scale brain, translate brain, rotate brain) don't work, probably because tkregister2 is deprecated in FS7 (I'm also not sure whether this error message after running tkregister2 is due to deprecation or I should fix something: "Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" tkregister2: interface: /media/kutato/Freesurfer/freesurfer/tktools/tkregister2.tcl tkregister.tcl: startup done") .
- Now, two other commands are suggested for checking/fixing talairach ( https://secure-web.cisco.com/1LO1j-HfWANah9bkDAzl63GP_S-czQD6Hh1KtmyxZmqUG8N...) (1) freeview -v bert/mri/T1.mgz -v bert/mri/brainmask.mgz:reg=bert/mri/transforms/talairach.xfm It loads the subject's T1 and the subject's brainmask, which is shifted compared to T1 due to applying the transformation. For me it tells nothing about the accuracy of talairach transform. The command also gives this message, that may be normal: "Not reading in xfm fileinfo"
(2) tkregisterfv --s bert --fstal --surf orig This command gives the following error: "ERROR: cannot find /media/kutato/Freesurfer/freesurfer/subjects/bert/surf/orig" While tkregister2 loads lh and rh wm surfs, it seems that tkregisterfv doesn't know the "--surf orig" option. I also tried "--surfs" option , no error message, but the surfaces were not loaded. It is also interesting that in tkregisterfv I see subject's volume as the MOVEABLE volume and the Talairach volume as the TARGET volume, while in tkregister2 I see the subject's volume as the TARGET volume and Talairach volume as a fuzzy MOVEABLE volume.
I'd really appreciate any help regarding the above. At present, I can check talairach using tkregister2 as earlier, but if correction is needed, I can't solve it with tkregister2 in my FS7.
Best, Gabor
Gabor Perlaki petzinger.gabor@gmail.com ezt írta (időpont: 2021. máj. 18., K, 18:04):
Dear all,
I tried to check the talairach transformation under Freesurfer 7 linux version (freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551). However, neither command works as expected.
the command "freeview -v bert/mri/T1.mgz -v bert/mri/brainmask.mgz:reg=bert/mri/transforms/talairach.xfm" gives the following message in the terminal: "Not reading in xfm fileinfo". Both T1 and brainmask is loaded, but the transformation seems to be not applied.
the command "tkregisterfv --s bert --fstal --surf orig" works only without the flag --surf.
the command "tkregister2 --s bert --fstal" gives the following messages:
Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary"
The green border is not shown, only the target and movable images are visible.
Any idea how to fix this? Best, Gabor
External Email - Use Caution
I've some subjects where talairach transform by FS7 was not optimal and thus eTIV was inaccurate. Because I'm interested in eTIV corrected volumes I need to correct it somehow. In my previous email I described my problems with correcting talairach transform in FS7. I'd really-really appreciate any suggestions/workaround to overcome this.
Gabor Perlaki petzinger.gabor@gmail.com ezt írta (időpont: 2021. máj. 19., Sze, 12:50):
I try to describe in more detail my problems with talairach check/correction in Freesurfer 7. In earlier versions, I used tkregister2 to check and correct talairach registration and it worked perfectly. The green line (orig surface of the subject) was very helpful in both checking and correcting the transformation. I can run tkregister2 under Freesurfer7 as well, but most of the buttons (scale brain, translate brain, rotate brain) don't work, probably because tkregister2 is deprecated in FS7 (I'm also not sure whether this error message after running tkregister2 is due to deprecation or I should fix something: "Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" tkregister2: interface: /media/kutato/Freesurfer/freesurfer/tktools/tkregister2.tcl tkregister.tcl: startup done") .
- Now, two other commands are suggested for checking/fixing talairach (
https://secure-web.cisco.com/17dG1hOi8KSYc03mNxyQC6C5YB2pFqLDye5REHgOsGO5Mnl...) (1) freeview -v bert/mri/T1.mgz -v bert/mri/brainmask.mgz:reg=bert/mri/transforms/talairach.xfm It loads the subject's T1 and the subject's brainmask, which is shifted compared to T1 due to applying the transformation. For me it tells nothing about the accuracy of talairach transform. The command also gives this message, that may be normal: "Not reading in xfm fileinfo"
(2) tkregisterfv --s bert --fstal --surf orig This command gives the following error: "ERROR: cannot find /media/kutato/Freesurfer/freesurfer/subjects/bert/surf/orig" While tkregister2 loads lh and rh wm surfs, it seems that tkregisterfv doesn't know the "--surf orig" option. I also tried "--surfs" option , no error message, but the surfaces were not loaded. It is also interesting that in tkregisterfv I see subject's volume as the MOVEABLE volume and the Talairach volume as the TARGET volume, while in tkregister2 I see the subject's volume as the TARGET volume and Talairach volume as a fuzzy MOVEABLE volume.
I'd really appreciate any help regarding the above. At present, I can check talairach using tkregister2 as earlier, but if correction is needed, I can't solve it with tkregister2 in my FS7.
Best, Gabor
Gabor Perlaki petzinger.gabor@gmail.com ezt írta (időpont: 2021. máj. 18., K, 18:04):
Dear all,
I tried to check the talairach transformation under Freesurfer 7 linux version (freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551). However, neither command works as expected.
the command "freeview -v bert/mri/T1.mgz -v bert/mri/brainmask.mgz:reg=bert/mri/transforms/talairach.xfm" gives the following message in the terminal: "Not reading in xfm fileinfo". Both T1 and brainmask is loaded, but the transformation seems to be not applied.
the command "tkregisterfv --s bert --fstal --surf orig" works only without the flag --surf.
the command "tkregister2 --s bert --fstal" gives the following messages:
Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary"
The green border is not shown, only the target and movable images are visible.
Any idea how to fix this? Best, Gabor
-- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.gabor@gmail.com
If the tkregisterfv command works without the --surf option, then just use that
On 5/18/2021 12:04 PM, Gabor Perlaki wrote:
External Email - Use Caution
Dear all,
I tried to check the talairach transformation under Freesurfer 7 linux version (freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551). However, neither command works as expected.
the command "freeview -v bert/mri/T1.mgz -v bert/mri/brainmask.mgz:reg=bert/mri/transforms/talairach.xfm" gives the following message in the terminal: "Not reading in xfm fileinfo". Both T1 and brainmask is loaded, but the transformation seems to be not applied.
the command "tkregisterfv --s bert --fstal --surf orig" works only without the flag --surf.
the command "tkregister2 --s bert --fstal" gives the following messages:
Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary"
The green border is not shown, only the target and movable images are visible.
Any idea how to fix this? Best, Gabor
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Gabor Perlaki