[caret-users] display myelin mapping results

Matt Glasser matt at ma-tea.com
Wed Feb 5 09:23:34 CST 2014


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
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>
>
>_______________________________________________
>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




More information about the caret-users mailing list