Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file.
In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail. Also is there a T/Z threshold applied to these clusters or just cluster-extent is used? In looking at the tutorials I see that 1.3 really is -log(0.05) so I do not think this relates to any sort of T or Z threshold but I just wanted to verify. Thanks, Ajay Also, when smoothed at 15mm the estimated smoothness was around 21mm. When lo On Friday, May 6, 2016, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Doug, > I wanted to figure out what is the minimum cluster extent for a given > monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the > following tutorial : > https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I > wanted to know if freesurfer estimates the smoothness for each subject's > cortical thickness for a hemisphere and then chooses the corresponding fwhm > folder or if by choosing lh 15mm in qdec the clusterwise values are taken > from the 15mm folder? Is the smoothness based on the smoothing kernel used > or the inherent smoothness of that particular measure (ie measuring the > smoothness of the input thicknesss image)? Is there a way to see what > cluster minimum is used? > > Thanks, > Ajay > > > On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Doug, >> Thanks for the clarification. So in the case of cortical thickness, >> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I >> should be getting similar results if everything is entered in the same >> fashion. This would be the approriate choice compared to mri_smooth. >> >> For mri_surf2surf I used the following command for smoothing LGI and >> cortical thickness and converting to .gii files. >> >> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval >> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex >> mris_convert -c rh.thickness.fwhm15.mgz >> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii >> >> >> 1) For cortical thickness does it make sense to use the --cortex option >> or should I specify a mask of some type (if so which) in mris_surf2surf? >> >> 2) For converting files to .gii should I be using rh.white as the option >> or should it be rh.pial? >> >> >> Best, >> Ajay >> >> >> >> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >> wrote: >> >>> Hi Doug, >>> Thanks for the quick reply. >>> >>> Is there a difference from qcache/mris_fwhm with mris_smooth and >>> mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness >>> analysis? >>> >>> Thanks, >>> Ajay >>> >>> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >>> wrote: >>> >>>> Hi Freesurfer Experts, >>>> Just as a followup through my reading i've come across posts which >>>> use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my >>>> cortical thickness analysis I would like to smooth all of my >>>> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a >>>> group analysis. After finding regions of difference, I would then like to >>>> use the ROI to extract each individual's mean thickness in the ROI in order >>>> to run a correlation with other measures. Based on this, I assume it would >>>> make sense to use smoothed data to identify the ROI and then use unsmoothed >>>> data for extracting actual thickness measures (does lh.thickness.fsaverage >>>> contain the original thickness or warped thickness values). >>>> >>>> I am unsure which smoothing is the most accurate or preferred. In >>>> using qcache the smoothness of the images do not seem to reach the filter >>>> level (based on the earlier email) so I am not sure if there is a >>>> freesurfer tool to check the smoothness level or if the qcache smoothness >>>> levels make sense for cortical thickness. >>>> >>>> Thanks, >>>> Ajay >>>> >>>> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >>>> wrote: >>>> >>>>> Hi Freesurfer Experts, >>>>> I am trying to understand the difference between qcache option and >>>>> mris_fwhm and which is appropriate for a cortical thickness analysis. I >>>>> processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii >>>>> (converted) files. I used an afni tool SurfFWHM to estimate the >>>>> smoothness >>>>> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 >>>>> and 20mm it was approximately 9.3-9.9 smoothness level. >>>>> >>>>> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i >>>>> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when >>>>> using SurfFWHM on the smae subject the smoothness was estimated at 11.25. >>>>> >>>>> >>>>> 1) I am not sure if the qcache or the mris_fwhm file is more >>>>> appropriate to use for a cortical thickness analysis. >>>>> >>>>> 2) For qdec if I select the 15mm option does it assume the smoothness >>>>> is 15mm when calculating monte carlo corrections? Would there be a >>>>> different way to estimate this since my smoothness at 15mm is closer to >>>>> 10mm? >>>>> >>>>> Thanks, >>>>> Ajay >>>>> >>>> >>>> >>> >> >
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