I'm not sure about the brain extraction. Seems worth a try. Unfortunately, I don't have permission to pass that data onto you; however, I did check in the structural directory of one of the Human Connectome Project (HCP), and looked at both of these files:
SUBJECT/T1w/T1wDividedByT2w.nii.gz SUBJECT/T1w/T1wDividedByT2w_ribbon.nii.gz Both appeared to be in the same orientation as the T1/T2 (i.e., x increases left to right, y increases posterior to anterior, y increases inferior to superior). So if your counterparts are not like that, then something may be amiss. On Feb 5, 2014, at 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
