Thank you very much! > On Mar 22, 2018, at 2:31 PM, Douglas Greve <dgr...@mgh.harvard.edu> wrote: > > you can view it with > tksurferfv fsaverage lh inflated -aparc -overlay conjunction.nii.gz -fminmax > 2 5 > tksurferfv is a front-end for freeview. You can change the thresholds in > freeview > > On 3/22/18 12:27 PM, nm644 wrote: >> Thank you for the quick reply. >> >> As you may be able to tell I'm a bit new at this so am still unsure about >> some things but yes a conjunction analysis is exactly what I want to do. >> Just a little more background, all the tasks are exactly the same in that >> they all have a null condition (set to 0 in all the paradigm files) with the >> same duration and the ON of all tasks also has the same duration across all >> tasks. I've also set the ON blocks in the 3 different paradigm files to be >> 1,2,3 instead of all being 1. >> >> Thus far I've done: >> >> 1) >> mkanalysis-sess \ >> -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ >> -event-related -paradigm para.tsv -nconditions 3 \ >> -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \ >> -analysis conjunction_analysis.lh -per-run -force >> >> 2) Create all the contrasts >> mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-1 -a 1 >> mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-2 -a 2 >> mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-3 -a 3 >> >> 3) Run the analysis with >> selxavg3-sess -s subj01 -analysis conjunction_analysis.lh \ >> -c task-1 \ >> -c task-2 \ >> -c task-3 >> >> Then cd into subj01/bold/conjunction_analysis.lh >> >> and finally >> >> 4) mri_concat >> mri_concat lang-cond-1/sig.nii.gz lang-cond-2/sig.nii.gz >> lang-cond-3/sig.nii.gz --conjunct >> --o conjunction.nii.gz >> >> Does this look right? Also, what would be the proper command to view the >> conjunction after running this? Sorry this is very long winded, I just want >> to make sure I'm doing everything properly. >> >> Thank you again! >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve >> <dgr...@mgh.harvard.edu> >> Sent: Tuesday, March 20, 2018 7:25:31 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Functional Overlap Map >> >> I'm not entirely sure what you are doing. It sounds like you have 3 >> different conditions and want to find out where the activation for all >> conditions overlaps. But what you have done is to combine all conditions >> into a single condition, so you are seeing where the average activation >> is, which is different than the overlap (and why it looks to have to >> much of an extent). To do what you want to do, you should model each >> condition as a separate condition in mkanalysis (ie, -nconditions 3 and >> change your paradigm file), set up 3 contrasts (one for each condition, >> ie, -a 1, -a 2, -a 3), then you will need to do a conjunction analysis >> (mri_concat con1/sig.nii.gz con2/sig.nii.gz con3/sig.nii.gz --conjunct >> --o conjunction.nii.gz). You can then view the conjunction with freeview >> (or tksurfer/tkmedit) >> >> >> On 03/20/2018 06:30 PM, nm644 wrote: >> > >> > Hello Freesurfer experts, >> > >> > My question may have already been solved in a previous thread. I have >> > three runs of block-design bold scans. All three are quite similar. >> > They all have only 2 blocks, one for rest and one for task. I’m trying >> > to create a functional map that displays where the functional >> > activation of these three runs overlap. I used the code below with no >> > errors: >> > >> > preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh >> > -mni305 -fwhm 5 -per-run >> > >> > mkanalysis-sess \ >> > >> > -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ >> > >> > -event-related -paradigm para.tsv -nconditions 1 \ >> > >> > -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \ >> > >> > -analysis TaskOverlap.lh -per-run -force >> > >> > mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1 >> > >> > selxavg3-sess -s subj01 -analysis TaskOverlap.lh >> > >> > And to display: >> > >> > tksurfer-sess -s subj01 \ >> > >> > -analysis TaskOverlap.lh \ >> > >> > -c con1 >> > >> > Or >> > >> > tksurfer-sess -s subj01 \ >> > >> > -analysis TaskOverlap.lh \ >> > >> > -c con1 -map fsig >> > >> > The problem is that when I view the output it seems that there’s far >> > more activation than there should be when trying to find mutual >> > overlap between the three tasks. If anyone has any suggestions it >> > would be much appreciated. >> > >> > Have a great day! >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIGaQ&c=cjytLXgP8ixuoHflwc-poQ&r=KqXv_tBMK5WvdtfVYgF6ItttJTffGZLOkpe8En34VKg&m=NmzK_XBGj_66WzMa8mbjmAj0s0d5OBz0aWNwoOjm320&s=bptg87NMt6k4IvnqeBEgS58-qA9VAFyhES5h8q5pdFc&e= >> . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> _______________________________________________ >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIBAg&c=cjytLXgP8ixuoHflwc-poQ&r=KqXv_tBMK5WvdtfVYgF6ItttJTffGZLOkpe8En34VKg&m=B5BNfVHCiR-qQVeCSQJSFB0-7CwT29dnFhWLONhM1gQ&s=RcCceYtZJ7pZgrI7AxG_G9t24H4lllzelqnB0R-rTSE&e= > . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail.
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