[caret-users] Question about MyelinMapping

Matt Glasser matt at ma-tea.com
Mon Nov 12 09:50:22 CST 2012

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.



On 11/12/12 8:42 AM, "Donna Dierker" <donna at 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 <yuichirosmz at 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
>> 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,
>> 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
>> 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 <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
>> 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
>> > 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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