[caret-users] Question about MyelinMapping
yuichirosmz at gmail.com
Mon Nov 12 06:56:44 CST 2012
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
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
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
In Fig.3, the regions around the central sulcus and occipital lobe are
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
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.
2012/11/9 Donna Dierker <donna at 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.:
> (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 <yuichirosmz at 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
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