Re: [Freesurfer] Comparing z score maps between 2 modalities in a group?

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 <fkm24@medschl.cam.ac.uk mailto:fkm24@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
<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
<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. > > > > > > > >
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