[caret-users] caret-users Digest, Vol 110, Issue 9

Colin Reveley cmr25 at sussex.ac.uk
Wed Nov 14 10:13:52 CST 2012


For what it's worth, if I was getting that result (and I'm sure I have at
some time) the first thing I'd check is that the origin of each volume
involved is the same, and that the origin is correct to align the surface
with the volumes.

in caret5 you can see if a surface is aligned by looking at "surface and
volume". if the surface is in the wrong place wrt the volumes that's
probably not good.

Even if that's not an issue, some of the volumes could have a differnt
origin. you check it in volume->edit volume attributes under the
coordinates tab. you can set the origin by reading it from another vol and
then saving. doubtless there's a command line way.

It could be as easy as that rather than a phase issue. It would be pretty
amazing if that resulted in exactly 0 in every voxel. but maybe.

In general I'd load each volume into caret, check the origin, and save it
again (as float). even if the origin is fine, load them all and save them
all so that caret has saved every volume involved and the niftii headers
are whatever caret wants. the ribbon volume. everything.

might work. might not. hope it does.


On 14 November 2012 10:25, <caret-users-request at brainvis.wustl.edu> wrote:

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> Today's Topics:
>
>    1. Re: Question about MyelinMapping (Matt Glasser)
>    2. Re: Question about MyelinMapping (Donna Dierker)
>
>
> ---------- Forwarded message ----------
> From: Matt Glasser <matt at ma-tea.com>
> To: "Caret, SureFit, and SuMS software users" <
> caret-users at brainvis.wustl.edu>
> Cc:
> Date: Wed, 14 Nov 2012 09:14:42 -0600
> Subject: Re: [caret-users] Question about MyelinMapping
> See my previous reply as to my guess what the problem is and how to show
> us that.
>
> Thanks,
> Matt.
>
> From: Yuichiro Shimizu <yuichirosmz at gmail.com>
> Reply-To: "Caret, SureFit, and SuMS software users" <
> caret-users at brainvis.wustl.edu>
> Date: Wednesday, November 14, 2012 3:45 AM
> To: "Caret, SureFit, and SuMS software users" <
> caret-users at brainvis.wustl.edu>
> Subject: Re: [caret-users] Question about MyelinMapping
>
> 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 <matt at ma-tea.com>
>
>> 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" <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
>> >>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 <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.:
>> >>
>> >>
>> >>
>> 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 <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
>> >> >   _______________________________________________
>> >> > caret-users mailing list
>> >> > caret-users at brainvis.wustl.edu
>> >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
>> >>
>> >>
>> >> _______________________________________________
>> >> caret-users mailing list
>> >> caret-users at brainvis.wustl.edu
>> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>> >>
>> >> _______________________________________________
>> >> caret-users mailing list
>> >> caret-users at brainvis.wustl.edu
>> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>> >
>> >
>> >_______________________________________________
>> >caret-users mailing list
>> >caret-users at brainvis.wustl.edu
>> >http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
>>
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
>
> _______________________________________________ caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
> ---------- Forwarded message ----------
> From: Donna Dierker <donna at brainvis.wustl.edu>
> To: "Caret, SureFit, and SuMS software users" <
> caret-users at brainvis.wustl.edu>
> Cc:
> Date: Wed, 14 Nov 2012 09:24:18 -0600
> Subject: Re: [caret-users] Question about MyelinMapping
> 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 <yuichirosmz at gmail.com>
> 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 <matt at ma-tea.com>
> > 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" <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
> > >>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 <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.:
> > >>
> > >>
> > >>
> 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 <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
> > >> >   _______________________________________________
> > >> > caret-users mailing list
> > >> > caret-users at brainvis.wustl.edu
> > >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > >>
> > >>
> > >> _______________________________________________
> > >> caret-users mailing list
> > >> caret-users at brainvis.wustl.edu
> > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > >>
> > >> _______________________________________________
> > >> caret-users mailing list
> > >> caret-users at brainvis.wustl.edu
> > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > >
> > >
> > >_______________________________________________
> > >caret-users mailing list
> > >caret-users at brainvis.wustl.edu
> > >http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >
> >
> > _______________________________________________
> > caret-users mailing list
> > caret-users at brainvis.wustl.edu
> > 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
> > caret-users at brainvis.wustl.edu
> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
>
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
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