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 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 <fk...@medschl.cam.ac.uk> 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 > > Best Wishes, > Elijah > > > > > > > Re: [Freesurfer] Comparing z score maps between 2 modalities in a group? > <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&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/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22> > Fri, 18 Nov 2016 08:19:47 -0800 > <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&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 > > > > 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 > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > athttp://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. > > > >
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