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.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 Best Wishes,Elijah
Re: [Freesurfer] Comparing z score maps between 2 modalities in a group?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. > > > > > > > > ______________________________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 > > 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. _________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.e du/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/grev ______________________________e/ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e du/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.