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? I initially thought that T or Z=1.3 is the threshold but in looking at tutorials I see that may be related to the color scale -log(0.05), so I am not sure if there is a minimum T/Z value to be included in the cluster or if I was correct at 1.3 is the threshold value (T or Z score or something else)?. Thanks, Ajay On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > 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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