[color=#000000]Hi Oliver,[/color]
[color=#000000]Those are interesting questions. Briefly:[/color]
[color=#000000](1) that should be fine (but see (3) below)[/color]
(2) yes (and it will switch the Gray/White/CSF ROIs to point to those new tissue class masks)
(3) none of the existing pipelines will apply the normalization spatial-transformation encoded in the y_*.nii files generated during normalization to your externally-defined Gray/White/CSF ROIs (the "Segmentation&Normalization" steps will create new Gray/White/CSF ROI files as part of the segmentation step, while the "Normalization" step only normalizes the functional or structural data leaving your Gray/White/CSF ROIs unchanged; see below for some alternative options)
(4) that should work perfectly fine but your Gray/White/CSF ROIs will remain unchanged (in subject-space) so you would need to manually (e.g. using SPM gui or batch commands) transform those files to MNI-space using the y_*.nii files generated during the normalization step.
Because (4) is somewhat time-consuming (and I imagine there would be other scenarios where users may want to use externally-defined tissue masks) I am also attaching a patch that includes a new "Structural Normalization with user-defined Gray/White/CSF masks" and "Functional Indirect Normalization with user-defined Gray/White/CSF masks" steps. These work just the same as the original "Structural Normalization" and "Functional Indirect Normalization" steps, respectively, but they will also keep any user-defined Gray/White/CSF ROIs (e.g. those that were imported from FreeSurfer) in the same space as your structural data. Internally they will simply apply in both cases the same non-linear transformations that is applied to the structural data to your Gray/White/CSF ROIs as well. Note that the assumption in both of these cases is that your externally-defined Gray/White/CSF masks will be in the same space as your structural data (which makes sense when importing FreeSurfer data). Let me know if you run into any issues with this patch (this patch is for release 18b, to install it simply copy the attached file to your conn distribution folder overwriting the file with the same name there)
Hope this helps
Alfonso
[i]Originally posted by Olivier Roy:[/i][quote]Hello,
Because I had trouble with skull-stripping with my raw T1 images (some skull often left in the posterior aspect of the brain), I decided to use the brainmask.mgz from Freesurfer which was properly skull-stripped. By using the brainmask, I also allowed Conn to import the segmentation files from Freesurfer. I then ran a modified version of the second volume-based preprocessing pipeline in Conn (see attached image): in brief, I just removed the "functional Creation of voxel-displacement map (VDM) for distortion correction" and replaced the realignment step with "functional Realignment & unwarp (subject motion estimation and correction)", effectively getting rid of the distortion correction part.
My questions are:
1. Since I used the brainmask.mgz which is already skull-stripped, will the skull-stripping part of the "functional Indirect Segmentation & Normalization" step have altered the image too much with the second skull-stripping step? So that I lose GM or CSF information for instance?
2. From what I understand, the "functional Indirect Segmentation & Normalization" step also resegment the Grey/White/CSF and overwrite those from Freesurfer. Is that true?
3. I want to co-register functional and structural volumes and then normalize to MNI while also keeping (and normalizing) the Grey/White/CSF segmentation from Freesurfer. If instead of the step "functional Indirect Segmentation & Normalization" I use the step "functional Indirect Normalization" (which also coregister structural and functional), will it also normalize the Grey/White/CSF segmentation from Freesurfer?
<span style="white-space: pre;"> </span>- I am asking this question because the "[u]functional Indirect Segmentation & Normalization[/u]" step gives as output the skull-stripped normalized structural volume, [b]normalized Grey/White/CSF masks[/b] and normalized functional volumes (all in MNI space) [u]whereas[/u] the "functional Indirect Normalization" step gives the [b]same thing (also seems to skull-strips; normal?) [/b][u]less the normalized Grey/White/CSF masks[/u].
4. Finally, if the answer to question #1 is that the second skull-stripping is problematic. Can I replace the step "functional Indirect Segmentation & Normalization" which skull-strips with the "functional Direct Coregistration to structural without reslicing" and subsequently "functional Direct Normalization" which do not seem to skull-strip again. How should I arrange the steps in the sequence in this case? Also in this case, how could I make sure that the Grey/White/CSF masks from Freesurfer get normalized to MNI?
Thank you and sorry for the long post,
Olivier[/quote]