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" <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> > > <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 > <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 -- 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
