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
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
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" greve@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 greve@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
I don't think that you need to do anything. If the tal reg checks out ok, then you can turn off the check when you run recon-all by adding -no-tal-check
On 11/11/2016 05:40 PM, John Anderson wrote:
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 *Sent:* Friday, November 11, 2016 at 4:42 PM *From:* "Douglas N Greve" greve@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" greve@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 greve@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
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 greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
John Anderson