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: [email protected] [[email protected]] on behalf of Donna Dierker [[email protected]] 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" <[email protected]> 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: [email protected] > [[email protected]] on behalf of Donna Dierker > [[email protected]] > 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" <[email protected]> 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: [email protected] >> [mailto:[email protected]] 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" <[email protected]> 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: [email protected] >>> [mailto:[email protected]] 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" <[email protected]> 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 >>>> [email protected] >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
