You need to rerun FreeSurfer after fixing the obliques, unfortunately. Peace,
Matt. On 3/19/14 9:46 AM, "Righart, Ruthger" <[email protected]> wrote: >Dear Matt, >Thank you for your reply to my question about myelin mapping. >There was indeed an issue with oblique s- and qforms (for the T2 >images) which I resolved. >I discovered for a subject however that still for frontal and occipital >areas t1/t2 ratios were not well mapped (there are large areas that give >values zero). Indeed, when I look at the volume-surface registration in >Caret the areas do not correspond well. > >I have several questions and would be very grateful if you could help >me: > >1. I wondered if for the original T1 the stereotaxic coordinates should >be set to 0,0,0 for the anterior commissure before running myelin >mapping. > >2. Should the original T1 be set in LPI orientation before myelin >mapping or is Caret doing this automatically? Might this be in conflict >with Freesurfer files and how to proceed? And should the original T1 and >T2 be skull-stripped? > >3. In the myelin mapping operations it is indicated that images are >best not resampled with trilinear interpolation. However, the >mri_convert rl mri/rawavg.mgz mri/ribbon.mgz ribbon.nii.gz command is >actually using trilinear interpolation. Is it possible and necessary to >do mri_convert with spline interpolation? > >Thank you very much for your suggestions! > >Best, >Ruthger > > >Le 2014-03-15 18:00, [email protected] a écrit : >> Send caret-users mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of caret-users digest..." >> >> >> Today's Topics: >> >> 1. Re: question about myelin mapping (Matt Glasser) >> >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 14 Mar 2014 11:42:29 -0500 >> From: Matt Glasser <[email protected]> >> To: "Caret, SureFit, and SuMS software users" >> <[email protected]> >> Subject: Re: [caret-users] question about myelin mapping >> Message-ID: <cf489b8d.c23b3%[email protected]> >> Content-Type: text/plain; charset="ISO-8859-1" >> >> Do the volumes align with the surfaces? Did you remove any oblique >> sforms? >> >> Peace, >> >> Matt. >> >> On 3/14/14 8:01 AM, "Righart, Ruthger" <[email protected]> >> wrote: >> >>>Dear Caret experts, >>> >>>I am using Caret for myelin mapping and I got first results for 4 >>>subjects. >>>After loading MyelinMapping.metric in Caret, for some of the subjects >>>large areas are missing, both for left and right hemisphere, >>>particularly in the occipital areas (i.e., the metric file seems to >>> have >>>missing values, however the corrected thickness metric displays >>> values >>>in these areas). >>> >>>Registration of T2-to-T1 is fine. The ribbon.nii.gz file and the >>>T1wDividedByT2w_ribbon.nii.gz seem fine as well, though the ribbon in >>>the occipital areas has fewer voxels than other areas (probably >>> because >>>these areas are relatively thin), and I wondered if this may cause a >>>problem for the final metric data. >>> >>>The caret_command -myelin-mapping script reports rather high >>>percentages of missing nodes : ?Out of 113592 cortex nodes, 50.37% >>> were >>>zero and needed correction. When reconstructing discarded nodes, >>> 68.88% >>>were zero and not used?. >>> >>>Thank you very much in advance for your time, any help would be very >>>much appreciated! > > > > > > >>> >>>Ruthger Righart >>> >>>_______________________________________________ >>>caret-users mailing list >>>[email protected] >>>http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> >> >> >> ------------------------------ >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> End of caret-users Digest, Vol 124, Issue 6 >> ******************************************* >_______________________________________________ >caret-users mailing list >[email protected] >http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
