Hi Doug, Ok this makes more sense now. In my case if I choose abs I would look at the max cdf < 0.05 for the corresponding cluster extent in the TH13 folder.
In terms of the |a-b|<0,05 does this mean that if I got results in blue it just means significant but with no directionality as to if A > B or B>A? I guess with the blue and red color bars I thought directionality was implied. Or would one need to do a subsequent one tailed test (Pos A>B; Neg B>A)d in order to determine directionality of thickness results? Thanks, Ajay On Mon, May 9, 2016 at 3:11 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? 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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