Hi Michael, while fslmaths has an option to do "2D" smoothing, this is still only smoothing in a slice of the volume and has the same problems as 3D smoothing (ie, smoothing across tissue types and sulci). The "2D" that FS implements with mris_volsmooth is along the cortical surface, which is unrelated to the volume axes. So, unfortunately, you do still have to do two analyses if you want a volume-based analysis with smoothing.
doug Michael Scheel wrote: > Hi Estephan, > > you don't necessarily have to rerun the full 1st level Analysis in total. > What you have to find out is which of your volumes is the one that > example_func is created from. > Normally this should be the middle timepoint fmri image of your > functional run (e.g. if you have 99 volumes then number 45 > will be taken as example_func) that's the default if you haven't > specified it otherwise. > You can use fslroi as a command to extract this volume for the above > example e.g.: > fslroi input_fmri.nii.gz middle_volume.nii.gz 44 1 > (fslroi starts counting from 0 thats why it is 44 instead of 45) > > 2D and 3D smoothing can also be done with > fslmaths see the -s and the -kernel option > > Best, Michael > On 23-Sep-09, at 6:52 PM, Douglas N Greve wrote: > >> >> >> Estephan Moana wrote: >>> So what I need to do is to run the 1st level FEAT as usual for the FSL >>> pipeline, and repeat this analysis for FS with the only difference >>> been to set the "Spatial smoothing FWHM" to zero on the pre-stats tab >>> of the FEAT GUI? >> yes >>> >>> Also, can you explain if this smoothing on the FEAT GUI is the 3D you >>> refer to? And how 2D smoothing is accomplished? >> Yes, this the 3D smoothing. 2D smoothing on the raw data is more >> difficult inside of feat. You'd have to use MC and then run >> mris_volsmooth (FS program) outside of FEAT, then pass FEAT the >> preprocessed data and tell it not to do MC or smoothing. >>> >>> Thank you. >>> >>> Estephan >>> >>> Douglas N Greve wrote: >>>> The example_func does not actually get smoothed, so smoothing itself >>>> will not affect the registration. 3D smoothing will smooth values >>>> from WM and CSF into gray and from across sulci into functionally >>>> distinct regions. For this reason we recommend not using 3D smoothing >>>> (or doing 2D smoothing on the surface). Unfortunately, this requires >>>> two different analyses. >>>> >>>> doug >>>> >>>> Estephan Moana wrote: >>>>> Hello all, I took the FS course last June at the OHBM in San >>>>> Francisco, and am now playing with it to get to know it better. One >>>>> of the slides on the talk about FSL-FS integration mentioned that >>>>> the input data (from FEAT) for the reg-feat2anat command should have >>>>> not been smoothed prior to registering to FS. >>>>> >>>>> Considering that FEAT 1st level analysis has a default of 5mm >>>>> spatial smoothing (and that's what I used on my data), it seems >>>>> counterintuitive to need to run a 1st level analysis again so the >>>>> output files are not spatially smoothed. >>>>> >>>>> So my questions are: 1) having the example_func file spatially >>>>> smoothed will necessarily hinder a proper registration to the FS >>>>> anatomical?; 2) if so, should I re-run all my FEAT 1st level >>>>> analysis without smoothing or is there any other way? >>>>> >>>>> I know this is quite a beginners question, but I could not find the >>>>> answers on the FS FAQ or the mailing list archives. I appreciate any >>>>> light on this. >>>>> >>>>> Regards, >>>>> >>>>> Estephan Moana, DDS >>>>> Graduate Student >>>>> Oral Biology PhD Program - Neurobiology track >>>>> School of Dentistry, UNC- Chapel Hill >>>>> 2140 Old Dental Building, CB# 7455 >>>>> Chapel Hill, NC 27599 >>>>> Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 >>>>> mo...@email.unc.edu <mailto:mo...@email.unc.edu> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> _______________________________________________ >> 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
