Thank you very much Doug,
Kindly, what do you suggest me to use instead of fslswapidim. What is your choice in this case? I highly appreciate your experience !
Bests,
John
John
Sent: Friday, November 11, 2016 at 4:42 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon all
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon all
On this volume as the head is almost at a 45deg angle perhaps causing
the nominal SI and AP to swap. Even after swap dim, the angle is pretty
extreme, but maybe better than the original so the tal check does not
fail. In general, I don't like to use swapdim as I'm afraid that it
might left-right rev the volume. In either case, you can manually check
the tal reg to see if it looks ok.
On 11/11/2016 03:56 PM, John Anderson wrote:
> Thank you Doug,
> Attched are to snapshots
> #1 is for the original T1 ( i.e. as aquired) and this image what
> output the error message mentioned in my previous email.
> #2 is after correcting the orientation using the command "*fslswapdim
> 001.nii RL PA IS T1-2mm_orientOK.nii"*
> I re run the same command "recon-all" on the newly corrected T1 image.
> The analysis is runnig fine right now, but when I checked the file
> "recon-all" I found similar error to what terminated my previous
> analysis. The differnce here is that the analysis didn't fail!
> Here is what I have in "recon.log"
> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0386, pval=0.0034 < threshold=0.0050)
> INFO: Attempting MINC mritotal to perform Talairach align
> Do I need to warry about this error? I appreciate any suggestion to
> improve analyzing this image.
> Bests,
> John
> *Sent:* Friday, November 11, 2016 at 3:19 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] recon all
> This can also happen if the head is oriented in a strange way. This can
> happen with older patients that tend to tilt their head back.
>
>
> On 11/10/2016 08:27 PM, Bruce Fischl wrote:
> > Hi John
> >
> > it means that the talairach transform that was computed was extremely
> > unlikely and deemed to be probably incorrect. Frequently this happens
> > if you start with images (like analyze) that don't contain accurate
> > direction cosine information. You can check this by bringing one of
> > the volumes in freeview and checking to make sure that the anatomical
> > directions we show
> > (e.g. anterior/posterior) correspond to the true anatomy. Sometimes
> > abnormal anatomiies like huge ventricles can also make it fail, but
> > you need to figure out which one it is before deciding what to do
> >
> > cheers
> > Bruce
> >
> >
> > On Fri, 11 Nov 2016, John Anderson wrote:
> >
> >> Dear Freesurfer experts,
> >> I ran the following command on a T1 image
> >> recon-all -subjid 089 -all -qcache
> >>
> >> and I got the following error message:
> >>
> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> >>
> >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> >> ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)
> >>
> >>
> >> I highly appreciate an explanation for the meaning of this error and
> >> how to
> >> fix it.
> >>
> >>
> >> Best
> >> John
> >>
> >>
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
the nominal SI and AP to swap. Even after swap dim, the angle is pretty
extreme, but maybe better than the original so the tal check does not
fail. In general, I don't like to use swapdim as I'm afraid that it
might left-right rev the volume. In either case, you can manually check
the tal reg to see if it looks ok.
On 11/11/2016 03:56 PM, John Anderson wrote:
> Thank you Doug,
> Attched are to snapshots
> #1 is for the original T1 ( i.e. as aquired) and this image what
> output the error message mentioned in my previous email.
> #2 is after correcting the orientation using the command "*fslswapdim
> 001.nii RL PA IS T1-2mm_orientOK.nii"*
> I re run the same command "recon-all" on the newly corrected T1 image.
> The analysis is runnig fine right now, but when I checked the file
> "recon-all" I found similar error to what terminated my previous
> analysis. The differnce here is that the analysis didn't fail!
> Here is what I have in "recon.log"
> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0386, pval=0.0034 < threshold=0.0050)
> INFO: Attempting MINC mritotal to perform Talairach align
> Do I need to warry about this error? I appreciate any suggestion to
> improve analyzing this image.
> Bests,
> John
> *Sent:* Friday, November 11, 2016 at 3:19 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] recon all
> This can also happen if the head is oriented in a strange way. This can
> happen with older patients that tend to tilt their head back.
>
>
> On 11/10/2016 08:27 PM, Bruce Fischl wrote:
> > Hi John
> >
> > it means that the talairach transform that was computed was extremely
> > unlikely and deemed to be probably incorrect. Frequently this happens
> > if you start with images (like analyze) that don't contain accurate
> > direction cosine information. You can check this by bringing one of
> > the volumes in freeview and checking to make sure that the anatomical
> > directions we show
> > (e.g. anterior/posterior) correspond to the true anatomy. Sometimes
> > abnormal anatomiies like huge ventricles can also make it fail, but
> > you need to figure out which one it is before deciding what to do
> >
> > cheers
> > Bruce
> >
> >
> > On Fri, 11 Nov 2016, John Anderson wrote:
> >
> >> Dear Freesurfer experts,
> >> I ran the following command on a T1 image
> >> recon-all -subjid 089 -all -qcache
> >>
> >> and I got the following error message:
> >>
> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> >>
> >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> >> ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)
> >>
> >>
> >> I highly appreciate an explanation for the meaning of this error and
> >> how to
> >> fix it.
> >>
> >>
> >> Best
> >> John
> >>
> >>
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
