I'm happy to hear it! Matt.
On 2/7/14 9:47 AM, "Cheng, Hu" <[email protected]> wrote: >Thank you Matt, all resolved. It's nice talking to you at UMN workshop. > >Regards, > >Hu > >-----Original Message----- >From: [email protected] >[mailto:[email protected]] 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" <[email protected]> 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: [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 > > >_______________________________________________ >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
