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.kurani@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.kurani@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.kurani@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.kurani@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.kurani@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