I know someone that uses something like what is below to avoid using tkregister: mri_convert $subject/mri/T1.mgz $subject/mri/T1.mnc mritotal -protocol icbm $subject/mri/T1.mnc $subject/mri/T1.xfm mv $subject/mri/transforms/talairach.xfm $subject/mri/transforms/oldtalairach.xfm cp $subject/mri/T1.xfm $1/mri/transforms/talairach.xfm

Doug and Nick can correct me if this isn't a good idea. You can do: mritotal -help to learn more about it. Allison

On Sat, 12 Jul 2008, Vina Goghari wrote:

Thanks Nick. I was wondering whether since this is a problem for all my subjects (n=70) is there anything else that could fix the problem (i.e. setting some parameter differently etc), so I wouldn't have to do it manually for every subject?

Nick Schmansky wrote:

...

Vina,

See this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

(you won't need the tutorial data, just use your subject)

Nick

On Sat, 2008-07-12 at 11:05 -0500, Vina Goghari wrote:

...

Hi all, I get this error:

Sat Jul 12 10:24:08 CDT 2008 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Sat Jul 12 10:24:08 CDT 2008 /pkg/bliss_all_labs/tricam/FEP_Aro/cbx02/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0069, pval=0.0000 < threshold=0.0050) Linux bliss 2.6.9-67.0.15.ELsmp #1 SMP Tue Apr 22 13:58:43 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Sat Jul 12 10:24:08 CDT 2008

So I viewed the talairach transform using tkregister2 and this is what I see for target and moveable. How would I go about fixing something like this:

See attached images.

Thanks, Vina

---

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Thanks everyone for consulting. I tried a random subset of 4 of the ~70 pts and I get the same error. I would say the attached is likely a typical SPGR shot.

Thanks!

Doug Greve wrote:

That would just do the conversion, it won't fix the problem. Does this happen with all your subjects? How is the quality of your T1s (the one you sent looks a little funny).

doug

Allison Stevens wrote:

...

I know someone that uses something like what is below to avoid using tkregister: mri_convert $subject/mri/T1.mgz $subject/mri/T1.mnc mritotal -protocol icbm $subject/mri/T1.mnc $subject/mri/T1.xfm mv $subject/mri/transforms/talairach.xfm $subject/mri/transforms/oldtalairach.xfm cp $subject/mri/T1.xfm $1/mri/transforms/talairach.xfm

Doug and Nick can correct me if this isn't a good idea. You can do: mritotal -help to learn more about it. Allison

On Sat, 12 Jul 2008, Vina Goghari wrote:

...

Thanks Nick. I was wondering whether since this is a problem for all my subjects (n=70) is there anything else that could fix the problem (i.e. setting some parameter differently etc), so I wouldn't have to do it manually for every subject?

Nick Schmansky wrote:

...

Vina,

See this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

(you won't need the tutorial data, just use your subject)

Nick

On Sat, 2008-07-12 at 11:05 -0500, Vina Goghari wrote:

...

Hi all, I get this error:

Sat Jul 12 10:24:08 CDT 2008 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Sat Jul 12 10:24:08 CDT 2008 /pkg/bliss_all_labs/tricam/FEP_Aro/cbx02/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0069, pval=0.0000 < threshold=0.0050) Linux bliss 2.6.9-67.0.15.ELsmp #1 SMP Tue Apr 22 13:58:43 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Sat Jul 12 10:24:08 CDT 2008

So I viewed the talairach transform using tkregister2 and this is what I see for target and moveable. How would I go about fixing something like this:

See attached images.

Thanks, Vina

---

---

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do you want to upload one of them for us to look at? On Wed, 16 Jul 2008, Vina Goghari wrote:

I would say it's pretty typical. I tried a random set of 4 subjects of the ~70 and I get the same error and similar mis-alignment between talairach and original.

Any thoughts?

Thanks, Vina

Doug Greve wrote:

...

That would just do the conversion, it won't fix the problem. Does this happen with all your subjects? How is the quality of your T1s (the one you sent looks a little funny).

doug

Allison Stevens wrote:

...

I know someone that uses something like what is below to avoid using tkregister: mri_convert $subject/mri/T1.mgz $subject/mri/T1.mnc mritotal -protocol icbm $subject/mri/T1.mnc $subject/mri/T1.xfm mv $subject/mri/transforms/talairach.xfm $subject/mri/transforms/oldtalairach.xfm cp $subject/mri/T1.xfm $1/mri/transforms/talairach.xfm

Doug and Nick can correct me if this isn't a good idea. You can do: mritotal -help to learn more about it. Allison

On Sat, 12 Jul 2008, Vina Goghari wrote:

...

Thanks Nick. I was wondering whether since this is a problem for all my subjects (n=70) is there anything else that could fix the problem (i.e. setting some parameter differently etc), so I wouldn't have to do it manually for every subject?

Nick Schmansky wrote:

...

Vina,

See this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

(you won't need the tutorial data, just use your subject)

Nick

On Sat, 2008-07-12 at 11:05 -0500, Vina Goghari wrote:

...

Hi all, I get this error:

Sat Jul 12 10:24:08 CDT 2008 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Sat Jul 12 10:24:08 CDT 2008 /pkg/bliss_all_labs/tricam/FEP_Aro/cbx02/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0069, pval=0.0000 < threshold=0.0050) Linux bliss 2.6.9-67.0.15.ELsmp #1 SMP Tue Apr 22 13:58:43 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Sat Jul 12 10:24:08 CDT 2008

So I viewed the talairach transform using tkregister2 and this is what I see for target and moveable. How would I go about fixing something like this:

See attached images.

Thanks, Vina

---

---

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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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to upload files, go here:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

you can copy me in the email as well.

On Wed, 2008-07-16 at 20:19 -0500, Vina Goghari wrote:

Yes, that would be great if you guys could take a look. What's the process to upload?

Thanks, Vina

Bruce Fischl wrote:

...

do you want to upload one of them for us to look at? On Wed, 16 Jul 2008, Vina Goghari wrote:

...

I would say it's pretty typical. I tried a random set of 4 subjects of the ~70 and I get the same error and similar mis-alignment between talairach and original.

Any thoughts?

Thanks, Vina

Doug Greve wrote:

...

That would just do the conversion, it won't fix the problem. Does this happen with all your subjects? How is the quality of your T1s (the one you sent looks a little funny).

doug

Allison Stevens wrote:

...

I know someone that uses something like what is below to avoid using tkregister: mri_convert $subject/mri/T1.mgz $subject/mri/T1.mnc mritotal -protocol icbm $subject/mri/T1.mnc $subject/mri/T1.xfm mv $subject/mri/transforms/talairach.xfm $subject/mri/transforms/oldtalairach.xfm cp $subject/mri/T1.xfm $1/mri/transforms/talairach.xfm

Doug and Nick can correct me if this isn't a good idea. You can do: mritotal -help to learn more about it. Allison

On Sat, 12 Jul 2008, Vina Goghari wrote:

...

Thanks Nick. I was wondering whether since this is a problem for all my subjects (n=70) is there anything else that could fix the problem (i.e. setting some parameter differently etc), so I wouldn't have to do it manually for every subject?

Nick Schmansky wrote:

> Vina, > > See this page: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > (you won't need the tutorial data, just use your subject) > > Nick > > > On Sat, 2008-07-12 at 11:05 -0500, Vina Goghari wrote: > >> Hi all, >> I get this error: >> >> Sat Jul 12 10:24:08 CDT 2008 >> talairach_avi done >> #-------------------------------------------- >> #@# Talairach Failure Detection Sat Jul 12 10:24:08 CDT 2008 >> /pkg/bliss_all_labs/tricam/FEP_Aro/cbx02/mri >> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm >> >> ERROR: talairach_afd: Talairach Transform: >> transforms/talairach.xfm ***FAILED*** (p=0.0069, pval=0.0000 < >> threshold=0.0050) >> Linux bliss 2.6.9-67.0.15.ELsmp #1 SMP Tue Apr 22 13:58:43 EDT >> 2008 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all exited with ERRORS at Sat Jul 12 10:24:08 CDT 2008 >> >> So I viewed the talairach transform using tkregister2 and this >> is what I see for target and moveable. How would I go about >> fixing something like this: >> >> See attached images. >> >> Thanks, >> Vina >> >> >> ------------------------------------------------------------------------ >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >

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