Freesurfer

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freesurfer subcortical segmentation
by ZhangBo 19 May '20

19 May '20

External Email - Use Caution Hi teams, Does freesurfer supports calculate subcortical volumes like globus pallidus internus, globus pallidus externa, subthalamic nucleus , ventral intermedius nucleus, like these areas? Thanks

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Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask
by Elena Pozzi 19 May '20

19 May '20

External Email - Use Caution Hi Douglas, Thank you very much for your answer. I tried the command you suggested and it did not seem to transfer the edits, so I added the flag -keep_mask_deletion_edits and that seems to work. Would you mind confirming that the final command mri_mask -keep_mask_deletion_edits brainmask.mgz norm.mgz brainmask.mgz is safe to run to transfer the edits (i.e., voxel deleted) from the norm.mgz to the brainmask.mgz? Thanks again! Elena

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Unable to visualize last Topics
by Ferraro, Pilar 19 May '20

19 May '20

External Email - Use Caution Hi Freesurfer experts, I’ve sent few days ago the Topic number 4 below (New PETSurfer Questions). I see from the summary that Topic number 5 contains the reply from Douglas, but I’m unable to visualize any topics after the number 4 (as you can see below). Would you able to resend the reply (Topic number 5), please? Sorry for the inconvenience and many thanks, Best, Pilar > Il giorno 7 mag 2020, alle ore 10:24 PM, freesurfer-request(a)nmr.mgh.harvard.edu ha scritto: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: HCPMMP1 parcellation to aseg (.mgz) (pooja prabhu) > 2. Re: HCPMMP1 parcellation to aseg (.mgz) (Douglas N. Greve) > 3. Re: HCPMMP1 parcellation to aseg (.mgz) (Glasser, Matthew) > 4. New PETSurfer Questions (Ferraro, Pilar) > 5. Re: New PETSurfer Questions (Douglas N. Greve) > 6. Re: HCPMMP1 parcellation to aseg (.mgz) (Douglas N. Greve) > 7. Re: Get Atlas surfaces in subject space (Douglas N. Greve) > 8. Compare individual to a group (Xiaojiang Yang) > 9. Re: Compare individual to a group (Douglas N. Greve) > 10. Re: Get Atlas surfaces in subject space (Ian Hardingham) > 11. FW: HCPMMP1 parcellation to aseg (.mgz) (Glasser, Matthew) > 12. Re: FreeSurfer 7 stable (Mina Rizkallah) > 13. Re: FreeSurfer 7 stable (Douglas N. Greve) > 14. Re: freesurfer 7.0.0 in a virtual machine... (fsbuild) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 May 2020 21:47:46 +0530 > From: pooja prabhu <prabhuppooja(a)gmail.com> > Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz) > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CANeOyK=NpztkVy3_N1wWPoHQuAFeDJ8rDFSLbf4HrAv-AJuFHA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > >> HCPMMP1 parcellation is multi modal parcellation >> We need the file something like we have for 'aparc' parcellation. >> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz) >> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot) > > > Date: Thu, May 7, 2020 at 2:16 PM > Subject: HCPMMP1 parcellation to aseg (.mgz) > To: <freesurfer(a)nmr.mgh.harvard.edu> > > > Hai list, >>> Can I get some insight on how to convert HCPMMP1 to aseg(provided we have annotation > files) for fsaverage brain? >>> For example: for aparc parcellation we use aparc2aseg and get > aparc+aseg.mgz. >>> Similarly I need for HCPMMP1. >>> Can someone help me with this? >>> Thank you > > From: "Glasser, Matthew" <glasserm(a)wustl.edu> > Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz) > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: Timothy Coalson <tsc5yc(a)mst.edu> > Message-ID: <29142489-F691-4E6E-A069-F7377D9C7A63(a)wustl.edu> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > That is our multi-modal parcellation. Tim has some instructions to get > data from the fs_LR mesh to fsaverage in GIFTI format. Doug perhaps you > can say how to convert from GIFTI to annot? > > Matt. > > > > -- > Thank You > Pooja Prabhu >

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Freesurfer hippocampal segmentation in patient with temporal lesion
by Linda Zhang 19 May '20

19 May '20

External Email - Use Caution Dear all, I have a subject for whom I need to segment the right hippocampal and amygdalar subfields. However, they have a significant white matter lesion and large ventricles in the right temporal lobe, such that skull-stripping consistently cuts away the cortex in that region, and subsequent aseg and surface reconstruction is inaccurate. My question is, does the hippocampal subfield module (I'm using the old segmentHA_T1.sh for consistency with our other subjects) use the aseg froom recon-all as a basis for its segmentation? If I just manually correct the hippocampus in the aseg and try running the subfields again, would it work? I've tried adjusting the skull-strip and no combination of wsthresh and no-wgcsaatlas has helped. I'm running FS6.0 on Ubuntu 18. Thank you! Regards, Linda

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Re: [Freesurfer] Robust Regression with Univariate LME
by Hua, Jessica 18 May '20

18 May '20

External Email - Use Caution Hi FreeSurfer Experts, Just bumping this item up. There are a couple of outliers in my data. I had winsorized the variable, but now I am trying to use robust regression to weight these outliers in my longitudinal analyses. In Matlab there is a robustfit function. Is there a way to modify the lme_fit_FS code to incorporate robust regression? Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 18 May '20

18 May '20

External Email - Use Caution Attached are the fsgd and Xg.dat files. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 18 May '20

18 May '20

External Email - Use Caution I was not sure how to modify the last line in your code in order to calculate adjusted values accounting for age, sex, and ICV for each participant (this is a three group design). Your code: There is not an easy way to do it, but you can do it in matlab cd glmdir X = load('Xg.dat'); y = load('perm.th30.abs.y.ocn.dat'); beta = inv(X'*X)*X'*y; yhat = X(:,[i j k ...]*beta([i j k ...]) where i j k ... indicate the factors you want keep in your data. Each factor gets a column in the design matrix (and a beta). If you need help figuring this out, send the fsgd file. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask
by Elena Pozzi 18 May '20

18 May '20

External Email - Use Caution Hi Douglas, I added some control points, but also and mostly made edits meant to fix the mask (e.g., deleted some voxels).

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vol2subfield single time course from multiple regions
by stdp82＠virgilio.it 18 May '20

18 May '20

External Email - Use Caution Hi list, vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sf ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol avgwfvol.mgz --o f2subf.nii.gz extracts the time course from each thalamic subregions. If I would like to merge multiple regions (e.g. --id 8115 --id 8116) and extract a single time course from them, which is the way? Thanks Stefano

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rh postcentral gyrus segmentation error
by KennethSPrice 18 May '20

18 May '20

External Email - Use Caution Hello Freesurfer Experts! I am looking for some guidance on improving the pial surface estimation at the right post-central gyrus. Looking at the aparc+aseg file, it is clear that the pial surface estimation missed some cortex. I have already experimented with different -wthresh values. Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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