Thank you Matt, all resolved. It's nice talking to you at UMN workshop. Regards,
Hu -----Original Message----- From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@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" <huch...@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-boun...@brainvis.wustl.edu >[caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker >[do...@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" <huch...@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-boun...@brainvis.wustl.edu >>[caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker >>[do...@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" <huch...@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-boun...@brainvis.wustl.edu >>>[mailto:caret-users-boun...@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" <huch...@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-boun...@brainvis.wustl.edu >>>> [mailto:caret-users-boun...@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" <huch...@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@brainvis.wustl.edu >>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > >_______________________________________________ >caret-users mailing list >caret-users@brainvis.wustl.edu >http://brainvis.wustl.edu/mailman/listinfo/caret-users >_______________________________________________ >caret-users mailing list >caret-users@brainvis.wustl.edu >http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
