I did not necessarily have any reservations about the method, I just did not want my reply to be misinterpreted as an actual endorsement. BTW, you might want to check out our recent pub on this topic
https://www.ncbi.nlm.nih.gov/pubmed/?term=greve+fdg On 11/18/2016 12:38 PM, Elijah Mak wrote: > > > Hi Doug, > > > Thanks for taking a look at the commands! I appreciate it. > > I would like to ask a further question about your concern/s regarding > this approach? > My aim was to have an analytical pipeline in Freesurfer that is > analogous to several studies (using VBM-type of analyses in SPM) where > they compared the relative severity of various pathological processes > measured from different modalities. For reference, > see:https://www.ncbi.nlm.nih.gov/pubmed/24951642 > <https://www.ncbi.nlm.nih.gov/pubmed/24951642> In that study, the > authors in that study were trying to examine whether hypometabolism > was relatively more severe compared to atrophy, and both > modalities(PET and T1) were Z-scored relative to controls, and then > compared against each other. > Best Wishes, > Elijah > > > On Fri, Nov 18, 2016 at 5:24 PM, Elijah Mak <[email protected] > <mailto:[email protected]>> wrote: > > > Hi Doug, > > Thanks for taking a look at the commands! > I would like to ask a further question about your concern/s > regarding this approach? My aim was to have an analytical pipeline > in Freesurfer that is analogous to several studies (using VBM-type > of analyses in SPM) where they compared the relative severity of > various pathological processes measured from different modalities. > I have attached a little screenshot for your reference. > For example, the authors in that study were trying to see whether > hypometabolism was relatively more severe compared to atrophy, and > both modalites (PET and T1) were Z-scored relative to controls, > and then compared against each other. Another study that has used > a similar technique is here: > https://www.ncbi.nlm.nih.gov/pubmed/24951642 > <https://www.ncbi.nlm.nih.gov/pubmed/24951642> > Best Wishes, > Elijah > > > Re: [Freesurfer] Comparing z score maps between 2 modalities in > a group? > > <http://www.mail-archive.com/[email protected]&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Comparing+z+score+maps+between+2+modalities+in+a+group%5C%3F%22&o=newest> > > Douglas N Greve > > <http://www.mail-archive.com/[email protected]&q=from:%22Douglas+N+Greve%22> > Fri, 18 Nov 2016 08:19:47 -0800 > > <http://www.mail-archive.com/[email protected]&q=date:20161118> > > Those commands look right, though I would do the smoothing before > computing the standard dev. Also, I don't know whether your > overall method is valid. > > On 11/15/2016 05:48 PM, Elijah Mak wrote: > Hi Freesurfer Team, > > > We would like to compare Z-scored surface maps between different > > modalities (MRI and PET) within a single group. 1 subject = 2 > measures. > > These are my steps so far, using mri_concat and > fscalc for the > generation of the Z score maps. Differences > between Z-score maps are > tested using the paired t-test approach > as outlined here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis > <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis> > > I > am not sure if my following steps are correct, so confirmation > will > be much appreciated, many thanks for your time and help! > > > // Generate mean/sd of healthy controls > > X > mri_concat --f > stacks_X_lh_HC_fsaverage --o group_mean_X_hc_lh.mgh --mean > > mri_concat --f stacks_X_lh_HC_fsaverage --o group_std_X_hc_lh.mgh > --std > > Y > mri_concat --f stacks__Y_HC_fsaverage --o > group_mean_Y_HC_lh.mgh --mean > mri_concat --f > stacks_Y_lh_HC_fsaverage --o group_std_Y_HC_lh.mgh --std > > QN: > Should smoothing be applied here or before? > > // Derive > individual Z-score map for X and Y > > X > for i in `cat list`; do > fscalc $i/surf/lh.X.fsaverage.mgh sub > group_mean_X_hc_lh.mgh div > group_std_X_hc_lh.mgh --o > $i/surf/lh.Z.thickness.fsaverage.mgh; > done > for i in `cat list; do fscalc $i/surf/rh.X.fsaverage.mgh > sub > group_mean_cth_hc_rh.mgh div group_std_X_hc_rh.mgh --o > > $i/surf/rh.Z.thickness. > fsaverage.mgh; done > > Y > for i in `cat list`; do fscalc > $i/surf/lh.Y.fsaverage.mgh sub > group_mean_X_hc_lh.mgh div > group_std_cth_hc_lh.mgh --o > $i/surf/lh.Z.fsaverage.mgh; done > > for i in `cat list; do fscalc $i/surf/rh.Y.fsaverage.mgh sub > > group_mean_Y_hc_rh.mgh div group_std_Y_hc_rh.mgh --o > > $i/surf/rh.Z.fsaverage.mgh; done > > > // Derive paired-difference > of Z scores between X and Y > > mri_concat --f stacks_XminusY_lh > --paired-diff --o concat_XminusY_lh.mgh > mri_concat --f > stacks_XminusY_rh --paired-diff --o concat_XminusY_rh.mgh > > // > Smooth concatenated maps of paired differences > > mri_surf2surf > --s fsaverage --hemi lh --fwhm 4 --sval > concat_XminusY_lh.mgh > --tval concat_XminusY_lh_sm4.mgh > > // Test significance of > paired differences within the group > > mri_glmfit --y > concat_XminusY_lh_sm4.mgh --fsgd fsgd_pairediff dods > --osgm > --surf fsaverage lh --cortex --glmdir > > I used the --osgm flag > as there are no covariates here. > > > > > > > > > _______________________________________________ > Freesurfer > mailing list > [email protected] > <mailto:[email protected]> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- > Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] > <mailto:[email protected]> Phone Number: 617-724-2358 Fax: > 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > _______________________________________________ Freesurfer mailing > list [email protected] > <mailto:[email protected]> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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. > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
