Re: [caret-users] Visualization in Caret
On Feb 5, 2014, at 4:19 PM, Eshita Shah wrote: > Hi Donna, > > I have tried changing the user threshold in the Metric Settings menu, but > nothing seems to change beyond +/- 0.05. There are a few blotches of orange > and yellow when it is at 0, and many sub-threshold regions (green) show up > when I put it up to 0.05, but nothing else changes as I move beyond 0.05 to > higher values (the orange slowly disappears, and it's all green). At least in Caret5 (less sure about workbench), thresholding won't work properly on the p-value, because thresholding assumes more extreme values -- further from zero -- are the more exceptional ones, whereas the opposite is true with p-values, where the closer to 0, the more rare. Since q is 1-p it should behave better in caret5 thresholding. If you threshold at q=.95, you should see less than if you threshold at q=.90. Like percentiles. > Is the value I'm changing the p or the q value? Or does that depend on what > column I have loaded in the "Threshold Adjustment" section? I'd display and threshold on both, for now, while you are trying to understand what the data shows. > If I am changing the q value, then does it mean that the regions that are > showing up have a p-value greater than 0.95 (since nothing changes after > 0.05) and thus they're not showing up as significant in my report? If you threshold at q=.95, you should see vertices colored that have p values of .05 or less, but you know none exist, because nothing survived in your report. Start at q=0.5. See some vertices. Probably lots of them. Then try q=0.75. You should see the clusters shrink now. Now 0.90. Anything? > Let me know if I am interpreting this the wrong way. > > Also, the coloring somewhat changes depending on the color palette I use. I > believe the default is PSYCH, but when I change it to PSYCH-NO-NONE, I see > orange blots in more regions than before (and of course what was grey earlier > turns dark blue). Why is that? The "new" orange blots appear in the same > positions as the sub-threshold green color does when I change the user > threshold to 0.05. It is how the palette is defined. There is a region of the color scale that blots out coloring near zero, while the NO-NONE removes that gap. While my memory fails me as to why,, I remember thinking there was something not quite intuitive about the one with the gap. Palettes are a matter of taste to some degree. Some are better with pos/neg values, while others are better with positive only, which is what you will have with your f-stats. For figures, I don't use p/q-values typically, but rather t- or f-maps. But for right now, you're doing a post-mortem on your analysis to see how close you were to having differences, so the q-maps will be useful for this purpose. > Lastly, how do I know which group is baseline and treatment? Does TFCE > automatically output the control group as the baseline, so the yellow would > indicate that the sulci are deeper in the treatment group vs. control? Or the > other way around? You used an ANOVA, which should produce a f-map -- all positive. There should be no +/- valence to it, unless I'm misunderstanding what you did. Out of curiosity, how many subjects were in each group? If you have only two groups and want to see where one group is deeper than the other, you can run a t-test instead of an anova. > Thanks for your help, > Eshita > > > > On Wed, Feb 5, 2014 at 5:58 AM, Donna Dierker > wrote: > Use the D/C: Metric Settings menu to adjust the threshold to .90, .85, etc. > until you start seeing something. If you see nothing, set it to zero and > start cranking up in larger increments. Q=1-p. > > > On Feb 4, 2014, at 8:09 PM, Eshita Shah wrote: > > > Hi Donna, > > > > What file specifically outputs the q-values and how far they are from > > significance? I think I am able to load the Q statistic column from the > > f-map onto the Conte69 atlas, but where should I be looking if I want to > > know what to change the threshold to? > > > > Thank you, > > Eshita > > > > > > On Tue, Feb 4, 2014 at 8:32 AM, Donna Dierker > > wrote: > > Yes, pretty much: I usually have a study directory into which I copy the > > Conte69 files. Then I rename the Conte69 spec to something more > > study-specific. I usually use the Conte69 inflated and very inflated for > > t-map visualization, along with mean group mid thickness (both > > medial/lateral surface views, but also overlaid as contours on volume > > slices). > > > > I don't usually use the TFCE column for visualization, and if I recall > > correctly, there might be p-value and q-value (1-p, which works better with > > the Caret thresholding) columns. This can tell you how close to > > significance you got. > > > > And yes: You use the D/C Overlay/Underlay surface menu to control what is > > displayed, which column, etc. > > > > > > On Feb 3, 2014, at 6:10 PM, Eshita Shah wrote: >
Re: [caret-users] Visualization in Caret
Hi Donna, I have tried changing the user threshold in the Metric Settings menu, but nothing seems to change beyond +/- 0.05. There are a few blotches of orange and yellow when it is at 0, and many sub-threshold regions (green) show up when I put it up to 0.05, but nothing else changes as I move beyond 0.05 to higher values (the orange slowly disappears, and it's all green). Is the value I'm changing the p or the q value? Or does that depend on what column I have loaded in the "Threshold Adjustment" section? If I am changing the q value, then does it mean that the regions that are showing up have a p-value greater than 0.95 (since nothing changes after 0.05) and thus they're not showing up as significant in my report? Let me know if I am interpreting this the wrong way. Also, the coloring somewhat changes depending on the color palette I use. I believe the default is PSYCH, but when I change it to PSYCH-NO-NONE, I see orange blots in more regions than before (and of course what was grey earlier turns dark blue). Why is that? The "new" orange blots appear in the same positions as the sub-threshold green color does when I change the user threshold to 0.05. Lastly, how do I know which group is baseline and treatment? Does TFCE automatically output the control group as the baseline, so the yellow would indicate that the sulci are deeper in the treatment group vs. control? Or the other way around? Thanks for your help, Eshita On Wed, Feb 5, 2014 at 5:58 AM, Donna Dierker wrote: > Use the D/C: Metric Settings menu to adjust the threshold to .90, .85, > etc. until you start seeing something. If you see nothing, set it to zero > and start cranking up in larger increments. Q=1-p. > > > On Feb 4, 2014, at 8:09 PM, Eshita Shah wrote: > > > Hi Donna, > > > > What file specifically outputs the q-values and how far they are from > significance? I think I am able to load the Q statistic column from the > f-map onto the Conte69 atlas, but where should I be looking if I want to > know what to change the threshold to? > > > > Thank you, > > Eshita > > > > > > On Tue, Feb 4, 2014 at 8:32 AM, Donna Dierker > wrote: > > Yes, pretty much: I usually have a study directory into which I copy > the Conte69 files. Then I rename the Conte69 spec to something more > study-specific. I usually use the Conte69 inflated and very inflated for > t-map visualization, along with mean group mid thickness (both > medial/lateral surface views, but also overlaid as contours on volume > slices). > > > > I don't usually use the TFCE column for visualization, and if I recall > correctly, there might be p-value and q-value (1-p, which works better with > the Caret thresholding) columns. This can tell you how close to > significance you got. > > > > And yes: You use the D/C Overlay/Underlay surface menu to control what > is displayed, which column, etc. > > > > > > On Feb 3, 2014, at 6:10 PM, Eshita Shah wrote: > > > > > Yes, that's what I was afraid of. I was expecting significant > differences between the two groups. But thanks for clarifying. > > > > > > I am still a bit confused on how exactly to load the metric files on > the Conte69 atlas. Do I open up the Conte69 spec and "add data files" in > the menu to open up TFCE files? And then do I overlay it using D/C --> > Overlay/Underlay Surfaces --> Primary Overlay, etc.? > > > > > > Again, thank you for all your help. > > > > > > Eshita > > > > > > > > > On Mon, Feb 3, 2014 at 3:49 PM, Donna Dierker < > donna.dier...@sbcglobal.net> wrote: > > > No, I think the problem is that nothing survived TFCE thresholding. > If it had, you would see an entry (or more) under the column heads > (Column, Thresh, Num-Nodes, etc.). There is no entry, which means nothing > survived. > > > > > > ColumnThresh Num-Nodes Area Area-Corrected COG-X > COG-Y > > > COG-Z P-Value > > > > > > TFCE P > > > > > > You can try loading your f-map > (ANOVA_29-01-14.OCD_CTRL.Depth.LH.fmap.significant.tfce.1.0E.2.0H.73730.metric) > and switch to the TFCE column, and apply thresholds corresponding to the > list of values right under the column heads, so you can see how close/far > you were. > > > > > > I am under the weather right now, so I will have another look at this > tomorrow, but I honestly think you are interpreting it correctly. If you > are like me, you probably are disappointed with these results. (There are > exceptions, of course.) > > > > > > > > > On Feb 3, 2014, at 4:37 PM, Eshita Shah wrote: > > > > > > > Donna, > > > > > > > > Thank you so much for your thorough response. What I'm worried about > as of now is the significance.report.txt file. I have uploaded it using the > link you provided, please let me know if there is anything unusual. When I > ran ANOVA without TFCE, I had rows of information right below the header, > as you mentioned. But for the TFCE report, I don't see anything similar. > Maybe I am interpreting it incorrectly? > > > > > > > > Thank you
Re: [caret-users] display myelin mapping results
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" 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" 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" 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:ca
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" 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" 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" 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 o
Re: [caret-users] libstdc++ version and caret5 (Timothy Coalson)
Colin, All I can tell you is that the Red Hat system we are using for compiling is Red Hat Enterprise Linux Server release 5.9 (Tikanga). John On Feb 5, 2014, at 8:00 AM, Colin Reveley wrote: > That's very helpful Tim/John thanks. > > Can I confirm it should (at least probably) run on RHEL6 and clones (CENTOS) > too? > > I can't test it it's for downstream colleagues. For delivering a product > using caret5 (and workbench). > > that's very handy the RHEL5 compilation. thanks. We had the same issue a year > ago on CENTOS5. downgrading caret worked for whatever reason. > > Colin > ___ > 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
Re: [caret-users] display myelin mapping results
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" 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" 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
Re: [caret-users] libstdc++ version and caret5 (Timothy Coalson)
That's very helpful Tim/John thanks. Can I confirm it should (at least probably) run on RHEL6 and clones (CENTOS) too? I can't test it it's for downstream colleagues. For delivering a product using caret5 (and workbench). that's very handy the RHEL5 compilation. thanks. We had the same issue a year ago on CENTOS5. downgrading caret worked for whatever reason. Colin ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
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" 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" 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
Re: [caret-users] Visualization in Caret
Use the D/C: Metric Settings menu to adjust the threshold to .90, .85, etc. until you start seeing something. If you see nothing, set it to zero and start cranking up in larger increments. Q=1-p. On Feb 4, 2014, at 8:09 PM, Eshita Shah wrote: > Hi Donna, > > What file specifically outputs the q-values and how far they are from > significance? I think I am able to load the Q statistic column from the f-map > onto the Conte69 atlas, but where should I be looking if I want to know what > to change the threshold to? > > Thank you, > Eshita > > > On Tue, Feb 4, 2014 at 8:32 AM, Donna Dierker > wrote: > Yes, pretty much: I usually have a study directory into which I copy the > Conte69 files. Then I rename the Conte69 spec to something more > study-specific. I usually use the Conte69 inflated and very inflated for > t-map visualization, along with mean group mid thickness (both medial/lateral > surface views, but also overlaid as contours on volume slices). > > I don't usually use the TFCE column for visualization, and if I recall > correctly, there might be p-value and q-value (1-p, which works better with > the Caret thresholding) columns. This can tell you how close to significance > you got. > > And yes: You use the D/C Overlay/Underlay surface menu to control what is > displayed, which column, etc. > > > On Feb 3, 2014, at 6:10 PM, Eshita Shah wrote: > > > Yes, that's what I was afraid of. I was expecting significant differences > > between the two groups. But thanks for clarifying. > > > > I am still a bit confused on how exactly to load the metric files on the > > Conte69 atlas. Do I open up the Conte69 spec and "add data files" in the > > menu to open up TFCE files? And then do I overlay it using D/C --> > > Overlay/Underlay Surfaces --> Primary Overlay, etc.? > > > > Again, thank you for all your help. > > > > Eshita > > > > > > On Mon, Feb 3, 2014 at 3:49 PM, Donna Dierker > > wrote: > > No, I think the problem is that nothing survived TFCE thresholding. If it > > had, you would see an entry (or more) under the column heads (Column, > > Thresh, Num-Nodes, etc.). There is no entry, which means nothing survived. > > > > ColumnThresh Num-Nodes Area Area-Corrected COG-X > > COG-Y > > COG-Z P-Value > > > > TFCE P > > > > You can try loading your f-map > > (ANOVA_29-01-14.OCD_CTRL.Depth.LH.fmap.significant.tfce.1.0E.2.0H.73730.metric) > > and switch to the TFCE column, and apply thresholds corresponding to the > > list of values right under the column heads, so you can see how close/far > > you were. > > > > I am under the weather right now, so I will have another look at this > > tomorrow, but I honestly think you are interpreting it correctly. If you > > are like me, you probably are disappointed with these results. (There are > > exceptions, of course.) > > > > > > On Feb 3, 2014, at 4:37 PM, Eshita Shah wrote: > > > > > Donna, > > > > > > Thank you so much for your thorough response. What I'm worried about as > > > of now is the significance.report.txt file. I have uploaded it using the > > > link you provided, please let me know if there is anything unusual. When > > > I ran ANOVA without TFCE, I had rows of information right below the > > > header, as you mentioned. But for the TFCE report, I don't see anything > > > similar. Maybe I am interpreting it incorrectly? > > > > > > Thank you, > > > Eshita > > > > > > > > > On Fri, Jan 31, 2014 at 1:15 PM, Donna Dierker > > > wrote: > > > On Jan 31, 2014, at 2:17 PM, Eshita Shah wrote: > > > > > >> Hi Donna, > > >> > > >> Yes! I was able to successfully get past the issue of JRE halting-- I > > >> just installed the latest JRE as Tim suggested, and added some options > > >> for garbage collection so that it would optimize memory use. Thank you > > >> for all your help! > > >> > > >> I have computed one mean midthickness for all my subjects, but > > >> specifically how do I overlay that onto an anatomical template? Would > > >> there be any advantage of using the NIFTI volume vs. using an average > > >> volume created from my subject pool? > > > > > > One advantage of using the template used for stereotaxic/volumetric > > > registration, if any was done, is that it is standard. Reviewers and > > > readers are more familiar with it, and don't have to understand how it > > > was generated. This is just for display/orientation -- not for analysis. > > > > > > Another is that you don't have the extra step of computing a mean volume. > > > > > >> f so, how would I be able to generate that average volume? > > > > > > I usually use AFNI's 3dMean when I need to do this, but FSL, SPM, and > > > other packages have similar features. Maybe wb_command supports it now. > > > You can probably do it in multiple steps with caret_command, but it's a > > > pain. > > > > > >> I am also a bit unclear on how to interpret and draw conclusions from > > >> the out
