[caret-users] display myelin mapping results

Matt Glasser matt at ma-tea.com
Fri Feb 7 10:17:34 CST 2014


I'm happy to hear it!

Matt.

On 2/7/14 9:47 AM, "Cheng, Hu" <hucheng at indiana.edu> wrote:

>Thank you Matt, all resolved. It's nice talking to you at UMN workshop.
>
>Regards,
>
>Hu
>
>-----Original Message-----
>From: caret-users-bounces at brainvis.wustl.edu
>[mailto:caret-users-bounces at brainvis.wustl.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, February 05, 2014 10:24 AM
>To: Caret, SureFit, and SuMS software users
>Subject: Re: [caret-users] display myelin mapping results
>
>There is probably some issue with the headers on these data.  You could
>try running fslreorient2std before running this pipeline (including
>FreeSurfer).
>
>Peace,
>
>Matt.
>
>On 2/5/14 8:52 AM, "Cheng, Hu" <hucheng at indiana.edu> wrote:
>
>>Thanks Donna. Yes, I did use overlay, I was able to see the
>>thickness.metric.
>>I'm not sure if I need to do brain extraction on T1w and T2w first. I
>>didn't do that. Is there anyway I can get one of your original T1w and
>>T2w images so that I can repeat the procedures on your data?
>>
>>Hu
>>
>>________________________________________
>>From: caret-users-bounces at brainvis.wustl.edu
>>[caret-users-bounces at brainvis.wustl.edu] on behalf of Donna Dierker
>>[donna at brainvis.wustl.edu]
>>Sent: Wednesday, February 05, 2014 9:42 AM
>>To: Caret, SureFit, and SuMS software users
>>Subject: Re: [caret-users] display myelin mapping results
>>
>>Note that after you do File: Open Data File and load
>>MyelinMapping.metric, you also have to select D/C: Overlay/Underlay -
>>Surface and change the primary overlay to the MyelinMapping column.
>>This won't change just by loading the file.  You may have done this,
>>but just making sure.  I wouldn't expect these maps to look alike.
>>
>>I really don't know about T1wDividedByT2w's orientation.  I'm not as
>>familiar with that pipeline as I'd like.  There is a chance it inverts
>>that way on purpose, to align with some canonical volume, but it's a
>>stretch.
>>
>>I will look at this again later with the data I do have and see if I
>>see the same thing.
>>
>>
>>On Feb 4, 2014, at 3:10 PM, "Cheng, Hu" <hucheng at indiana.edu> wrote:
>>
>>> Hi Donna,
>>>
>>> I was able to visualize the metric file (e.g. thickness.metric) on
>>>the individual's surface, but I think there is a problem with the
>>>myelin mapping result. I couldn't see any change after I loaded
>>>MyelinMapping.metric. I tried to visualize T1w and T2w images, they
>>>aligned well with each other, but not with T1wDividedByT2w, which is
>>>inverted in AP and SI directions. Do you have any clues of what went
>>>wrong?
>>> Thanks!
>>>
>>> Hu
>>>
>>> ________________________________________
>>> From: caret-users-bounces at brainvis.wustl.edu
>>>[caret-users-bounces at brainvis.wustl.edu] on behalf of Donna Dierker
>>>[donna at brainvis.wustl.edu]
>>> Sent: Thursday, January 30, 2014 11:22 AM
>>> To: Caret, SureFit, and SuMS software users
>>> Subject: Re: [caret-users] display myelin mapping results
>>>
>>> Hmmm.  I inspected a directory here I know has been through myelin
>>>mapping, and it has files named like the ones you list below, but it
>>>also has surface files.  (Mine has both *surf.gii surfaces and
>>>*.coord.gii/*.topo.gii pairs.  May have had other processing.)  But I
>>>did confirm these surfaces are on native mesh, which means you canNOT
>>>view them on the Conte69 surface.  They are not on the same mesh.
>>>
>>> Spec files can be created and added to via script (e.g., wb_command
>>>or caret_command, depending on whether you're using Caret5 or
>>>workbench), if all you need to do is view the maps on the individuals'
>>>surfaces.
>>>
>>> There is a freesurfer_to_fs_LR script that uses the Freesurfer
>>>registration to get your surfaces on 164k_fs_LR standard mesh.  It
>>>creates spec files that can be used with Caret5, but they do not work
>>>with workbench.
>>>
>>> We will be releasing a version of the HCP pipeline to the public --
>>>probably sometime this year, but things are still being finalized, so
>>>it's not ready to roll yet.  Those scripts will produce spec files
>>>that work with workbench.
>>>
>>> It's not clear how important the standard mesh is to you, but if you
>>>want to do cross-subject analyses, you'll probably need it.
>>>
>>>
>>> On Jan 30, 2014, at 8:27 AM, "Cheng, Hu" <hucheng at indiana.edu> wrote:
>>>
>>>> Thank you Donna,
>>>>
>>>> The result is on individual's surface. I tried that command but got
>>>>nothing. There is no spec or scene file under the directory. As
>>>>stated in the document:
>>>> The output files are:
>>>> L.MyelinMapping.metric
>>>> R.MyelinMapping.metric
>>>> T1wDividedByT2w.nii.gz
>>>> T1wDividedByT2w_ribbon.nii.gz
>>>>
>>>> These include a metric file for each hemisphere with these columns:
>>>>a raw myelin map (with no outlier correction) a corrected myelin map,
>>>>a smoothed myelin map, and a cortical thickness corrected for surface
>>>>curvature.  Additional outputs are the T1w/T2w volume, and the same
>>>>volume containing only the voxels of the cortical ribbon.
>>>>
>>>> Regards,
>>>>
>>>> Hu
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: caret-users-bounces at brainvis.wustl.edu
>>>>[mailto:caret-users-bounces at brainvis.wustl.edu] On Behalf Of Donna
>>>>Dierker
>>>> Sent: Wednesday, January 29, 2014 4:51 PM
>>>> To: Caret, SureFit, and SuMS software users
>>>> Subject: Re: [caret-users] display myelin mapping results
>>>>
>>>> You could do that, but assuming the myelin mapping results output
>>>>individual myelin maps on the 164k_fs_LR standard mesh (or 32k), then
>>>>you could actually look at them on the Conte69 atlas (e.g., inflated
>>>>surface).  You could have multiple subjects' maps loaded and toggle
>>>>from one to the other.
>>>>
>>>> But if you want to click on the maps and "ID node" spots on the
>>>>midthickness surface, for example, so you could see what the
>>>>individual anatomy looks like, and how its contours overlay on the
>>>>T1/T2, then you're better off using an individual spec file.
>>>>
>>>> To be honest, I'm not familiar with myelin mapping yet, but I am
>>>>trying to learn more about it.  Assuming you are on a Linux or MacOSX
>>>>machine, could you do this command:
>>>>
>>>> find /directory/where/my/myelin/mapping/results/are/located | sort >
>>>>/tmp/myelinoutputfiles.txt
>>>>
>>>> ... then upload the resulting /tmp/myelinoutputfiles.txt here:
>>>>
>>>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>>>
>>>> I'm wondering if spec or scene files already exist, and want to rule
>>>>it out before you generate your own.
>>>>
>>>>
>>>> On Jan 29, 2014, at 2:59 PM, "Cheng, Hu" <hucheng at indiana.edu> wrote:
>>>>
>>>>> Hi Donna,
>>>>>
>>>>> I followed the procedures in Myelin_Mapping_Documentation_v2.doc
>>>>>and finished processing my own data. I just wonder how to display
>>>>>the results just as viewing conte69 results. Should I copy their
>>>>>spec file and replace all the files?
>>>>> Thank you very much!
>>>>>
>>>>> Regards,
>>>>>
>>>>> Hu
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: caret-users-bounces at brainvis.wustl.edu
>>>>> [mailto:caret-users-bounces at brainvis.wustl.edu] On Behalf Of Donna
>>>>> Dierker
>>>>> Sent: Monday, January 20, 2014 6:18 PM
>>>>> To: Caret, SureFit, and SuMS software users
>>>>> Subject: Re: [caret-users] only got one hemisphere from surefit
>>>>>
>>>>> SureFit only segments one hemisphere at a time.  You need to crop
>>>>>to a left or right hemisphere and run them separately.
>>>>>
>>>>>
>>>>> On Jan 20, 2014, at 3:36 PM, "Cheng, Hu" <hucheng at indiana.edu> wrote:
>>>>>
>>>>>> Dear Caret User,
>>>>>>
>>>>>> I'm running Caret on a 64-bit Windows. I tried to segment an
>>>>>>individual's T1w anatomy using surefit. I set the origin at AC and
>>>>>>select "both" in structure.  However, I only got left hemisphere
>>>>>>segmented. The inflated surface is only half of the brain. What did
>>>>>>I do wrong?
>>>>>> Thanks for your help!
>>>>>>
>>>>>> Hu Cheng, Ph.D., DABMP
>>>>>> MRI Physicist, Imaging Research Facility Department of
>>>>>> Psychological and Brain Sciences Indiana University Bloomington, IN
>>>>>>47405 Tel.
>>>>>> 812-856-2518 Fax. 812-855-4691
>>>>>>
>>>>>> _______________________________________________
>>>>>> caret-users mailing list
>>>>>> caret-users at brainvis.wustl.edu
>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>>
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>>>>
>>>>
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>>
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