I wonder if your sform has obliques in it. I agree that a screenshot would be helpful, together with verifying that the surfaces and T1w and T2w volumes are well aligned in some other screenshots.
Peace, Matt. On 11/12/12 8:42 AM, "Donna Dierker" <do...@brainvis.wustl.edu> wrote: >Okay, if you're using a down sampled map (which might be in the myelin >mapping pipeline -- just not sure), then all bets are off. I would think >you'd need a downsampled spec file. Maybe one exists in sumsdb. Try >searching for the number of nodes you have. Use the "Show Parent" >feature from the sumsdb drop-down menu, if needed. > >It's not clear to me whether you did "File: Open Data File: Metric file" >at any point. After adding the file to the spec file, and clicking open, >it should have the same effect, but that was still hazy for me. But it >is probably the resolution issue, as you say. > >There is variability in myelin maps, but your result sounds suspicious. >Attach a capture. > > >On Nov 12, 2012, at 6:56 AM, 清水祐一郎 <yuichiro...@gmail.com> wrote: > >> Thank you for a quick reply. >> >> I found and downloaded the files that you mentioned. >> Using the files, I've tried mapping. >> I added R.MyelinMapping.metric to the >>Fig4_fsaverage_Conte-69.164k_fs_LR.spec, and in the Display Control, >>tried to set the metric file. >> But, I couldn't find the metric file and overlay the >>R.MyelinMapping.metric onto the FIDUCIAL >>fsaverage.L.midthickness_mni.mws_flip-x.164k_fs_LR.coord.gii. >> >> On the other hand, I also tried mapping L.MyelinMapping.metric onto the >>left fiducial coordinates. >> >> I completely obeyed the process described in the website, >>CaretOperation, using the downloaded data. >> And then, I made a spec file below. >> First, I added the topo and coord files. >> There were topo.gii and coord.gii files so I renamed the files eraseing >>.gii. >> Then I changed the spec file's resolution. I set the number of nodes, >>2562. >> Finally, I overlayed L.MyelinMapping.metric >> >> But, the myelin mapping pattern is different from the Figure 3 (Glasser >>et al. 2011). >> In Fig.3, the regions around the central sulcus and occipital lobe are >>strongly mylinated. >> But, the result that I obtained showed the pattern that the middle and >>upper part of >> the brain is myelinated. >> >> Is there any wrong procedure? >> >> >> Furthermore, I analyzed other images that were taken in our MRI scanner. >> >> MRI scanner (3 Tesla GE Healthcare Signa HDxt) >> T1w images: SPGR TR 7400 ms, TE 3 ms, TI 600 ms, FA = 10, FOV = 256 x >>256, 1 mm slice >> T2w images: CUBE(XETA) TR 2500 ms, TE 80 ms, FOV = 256 x 256, 1 mm >>slice >> >> I obtained plausible thickness maps, but the intensity in myelin.metric >>are all zero! >> Although the scanning condition seems to be the same as the paper, the >>results are apparently wrong. >> I'm at a loss what is wrong. >> >> I appreciate your kindful instruction. >> >> Yuichiro Shimizu >> >> 2012/11/9 Donna Dierker <do...@brainvis.wustl.edu> >> Matt might get to this, but here are some clues based on how I'd >>proceed in your shoes: >> >> Find a figure in one of our papers like the one I want to make, e.g.: >> >> >>http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8288739&archive_na >>me=Fig4_fsaverage_Conte-69.164k_fs_LR.spec >> >> (I couldn't find the sumsdb dir for Matt's myelin paper, but I think >>David's paper will work for the purposes of jumpstarting you into a >>visualization spec.) >> >> Fig 4D from the drop-down menu could just as easily have a myelin map >>overlaid on it. >> >> Download that spec and overlay your maps on the Conte69 inflated >>surface. >> >> This is probably not as step-by-step as you would like, but this >>happens to be a very busy time for everyone. If you run into trouble, >>post again. >> >> >> On Nov 9, 2012, at 12:31 AM, 清水祐一郎 <yuichiro...@gmail.com> wrote: >> >> > Hello >> > >> > According to the web page Caret operation:MyelinMapping, I've >>obtained the final results: L.MyelinMapping.metric, >>R.MyelinMapping.metric, T1wdividedbyT2w.nii.gz, and >>T1wdividedbyT2w_ribbon.nii.gz. >> > The detail condition is described below. >> > >> > -information about my analysis procedure >> > individual MRI data: downloaded from NAMIC >> > recon-all by FreeSurfer(stable5-20110522) in CentOS5.5 64 bit >> > myelinmapping by Caret5 ver.5.65 in Windows7 64 bit >> > >> > Through the processes, no error message was displayed. >> > Furthermore, I confirmed that the T1wdividedbyT2w.nii.gz image is >>comparable with an other result image, the original T1w image divided by >>the registered T2w imageby by ImCalc in spm8. >> > >> > However, I have trouble in viewing the result of MyelinMapping.metric >>on the inflated surface as shown in the paper (Glasser et al. 2012) >> > >> > When I try to open the L.MyelinMapping.metric, 'Creat Spec File' >>window is open. >> > I don't know how to make a spec file. >> > >> > Tentatively, I set the subject name and chose 'left' as the structure. >> > Next, I pushed the OK button for 'creat new column' for left smoothed >>corrected myelin map. >> > Finally, I got an error message, Error: L.MyelinMapping.metric: >>Contains different number of nodes than. >> > >> > In addition to this, I tried 'Add Document File to Spec File'. >> > I added a topo.file, a coord.file, and a structural 3D image. >> > It did not work, too. >> > >> > Because I'm a newcomer as Caret user, I'd like detailed information. >> > >> > Thank you in advance. >> > >> > Yuichiro Shimizu >> > _______________________________________________ >> > caret-users mailing list >> > caret-users@brainvis.wustl.edu >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > >_______________________________________________ >caret-users mailing list >caret-users@brainvis.wustl.edu >http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
