Hi Yuichiro, I think the most efficient thing is for you to upload your T1 & T2 NIFTI volumes here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi Just the original T1/T2. We can look at the header and see if Matt's hunch was right. Donna On Nov 14, 2012, at 3:45 AM, Yuichiro Shimizu <[email protected]> wrote: > Thank you for your reply. > > I did the Caret Operation process for the downloaded data from NAMIC again. > Then I found a typing error of file extension in the process. > Correcting it, I could finally obtain the same figure as the Fig. 3 (Glasser > et al. 2011). > I'm very sorry for my careless mistake. > > myelin capture (file name: downloadeddata_myelin) > thickness capture (file name: downloadeddata_thickness) > > But there still is a problem. > When I analyzed the data that were taken in our MRI scanner in the same > manner, > the resultant MyelinMapping.metric files contain only the number, zero. > (while thickness.metric contains plausible values) > > myelin capture (file name: mydata_myelin) > thickness capture (file name: mydata_thickness) > > I compared all the resultant images in the process, i.e., T1w, OrigT2w, > OrigT2w_conform_RAS, T2w_conform_RAS2T1wbb... > Only one difference that I found is the direction of T1w, T2w images in > FSLview. > > T1w FSLview / NAMIC (file name: downloadeddata_originalT1w) > T2w FSLview / NAMIC (file name: downloadeddata_T2w) > > T1w FSLview / our data (file name: mydata_originalT1w) > T2w FSLview / our data (file name: mydata_T2w) > > I wonder if the phase/frequency encoding caused the difference. > Is there any other point I have to check or change? > > Sincerely. > > Yuichiro Shimizu > > 2012/11/13 Matt Glasser <[email protected]> > 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" <[email protected]> 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 <[email protected]> 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 <[email protected]> > >> 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 <[email protected]> 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 > >> > [email protected] > >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> _______________________________________________ > >> 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 > > > > > >_______________________________________________ > >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 > > <downloadeddata_myelin.jpg><downloadeddata_originalT1w.jpg><downloadeddata_T2w.jpg><downloadeddata_thickness.jpg><mydata_myelin.jpg><mydata_originalT1w.jpg><mydata_T2w.jpg><mydata_thickness.jpg>_______________________________________________ > 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
