On 06/04/2015 11:55 AM, std...@virgilio.it wrote: > I'm sorry Doug but I should run mkanalysis-sess -mni305 for both right > and left thalamus (which are taskreg). > > Specifically, I'm performing > > mkanalysis-sess -analysis fc.lthalseed.surf.lh -surface fsaverage lh > -fwhm 5 -notask -taskreg L_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg > wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run > mkanalysis-sess -analysis fc.rthalseed.surf.rh -surface fsaverage rh > -fwhm 5 -notask -taskreg R_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg > wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run > > > for mni305 I should performed as above? > > mkanalysis-sess -analysis fc.lthalseed.mni305 -mni305 -fwhm 5 -notask > -taskreg L_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 > -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run > mkanalysis-sess -analysis fc.rthalseed.mni305 -mni305 -fwhm 5 -notask > -taskreg R_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 > -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run Yes, that looks like it will work. doug > > Thanks, > > > Stefano > > > > > ----Messaggio originale---- > Da: gr...@nmr.mgh.harvard.edu > Data: 4-giu-2015 16.43 > A: <freesurfer@nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: mni305 volume-based analysis > > The mkanalysis-sess command should be almost identical for all 3 > analyses. The only thing you would change is "-surf fsaverage lh" "-surf > fsaverage rh" or "-mni305" > > doug > > On 06/04/2015 03:21 AM, std...@virgilio.it wrote: > > > > Hi list, > > > > > > I 'm continuing to have problem to run mni305 volume-based analysis. > > > > I have read the guide > > > (http://freesurfer.net/fswiki/FsFastFunctionalConnectivityWalkthrough?highlight=%28mkanalysis%5C-sess%29%7C%28connectivity%29). > > > > It explains that separate mkanalysis-sess commands will need to be run > > for the each hemisphere and for the mni305 volume-based analysis. > > > > I have no problem for right and left. > > > > However, I do not understand the line for mni305: what is it for > -taskreg? > > > > Thanks, > > > > > > Stefano > > > > > > > > > > Douglas Greve Mon, 25 May 2015 15:31:34 -0700 > > > > Have you looked at the documentation for FC analysis in FSFAST? It > > gives sample mkanalysis-sess commands for lh. They are basically the > > same for rh and mni305 > > > > On 5/22/15 7:19 PM, std...@virgilio.it wrote: > > > > Hi list, > > > > I'm configuring mkanalysis-sess to configure an analysis for FC data by > > > > FS-FAST. > > > > I do not understand how I can perform mni305 volume-based analysis. > > > > How can I configure an analysis for mni305? Specifically, which is the > > paradigm > > > > file in > > > > -taskreg? How is the command for group level preprocessing using seg305? > > > > I have performed these step: > > > > 1. Analyze anatomicals in FreeSurfer (recon-all) > > > > 2. Create subjectname file. > > > > 3. Preprocessing > > > > preproc-sess -s Sess01 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest > > > > -per-run > > > > 4. Parameters configuration to creates a text file describing the FC > > seed for > > > > an individual. > > > > fcseed-config -segid 10 -fcname L_Thalamus.dat -fsd rest -mean -cfg > > > > mean.L_Thalamus.config > > > > fcseed-config -segid 49 -fcname R_Thalamus.dat -fsd rest -mean -cfg > > > > mean.R_Thalamus.config > > > > 5. fcseed-sess -s Sessid -cfg mean.R_Thalamus.config > > > > fcseed-sess -s Sessid -cfg mean.L_Thalamus.config > > > > 6. Create nuisance variables: > > > > fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config > > > > fcseed-sess -s sessionid -cfg wm.config > > > > fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config > > > > fcseed-sess -s sessionid -cfg vcsf.config > > > > 7. selxavg3-sess -s Sessid -a fc.lthalseed.surf.lh > > > > selxavg3-sess -s Sessid -a fc.rthalseed.surf.lh > > > > Thanks > > > > Stefano > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 > http://www.partners.org/complianceline . 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
