On 05/09/2016 04:11 PM, Ajay Kurani 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. It is the overall alpha, but the test is unsigned, so it is 5% for |A-B|>0 > > 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)?. In the simulation, the cluster-forming threshold (eg, p<.01,sig>2) is converted into a z-score and used to threshold the smoothed z-map. No t-thresholding is done,. > > Thanks, > Ajay > > On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani <dr.ajay.kur...@gmail.com > <mailto: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 > <mailto: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 > > > > > > > > > _______________________________________________ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
