[Freesurfer] Non-matching results for area ROI group analysis using two different approaches

Dear Freesurfer experts I have run an ROI analysis in Freesurfer using two different strategies and I would have expected the results to be the same (or similar), but they are not and I don't really understand why. I have an ROI that I obtained from an atlas in MNI space and projected to the

[Freesurfer] Non-matching ROI areal measures using mri_segstats and mris_anatomical_stats (2nd post)

I am reposting this message, as I didn't get any answer so far: - Dear Freesurfer experts I have run a group ROI analysis comparing cortical thickness and area between two groups of subject. I did this in two dif

Re: [Freesurfer] Non-matching ROI areal measures using mri_segstats and mris_anatomical_stats (2nd post)

et=windows-1252; format=flowed > > Sorry, I thought I had answered this (or something like it) recently. > When transforming area (or volume) with mri_surf2surf you have to turn > on jacobian correction with --jac. Try that and see if the results are > similar > doug > > > On 9/

[Freesurfer] flirt.fsl error (NEWMAT::SingularException) when running bbregister in Freesurfer 7.0.0

External Email - Use Caution Hi, I just installed freesurfer v7 and I'm getting an error in a script that calls bbregister with the --fslmat and --init-fsl options. This error does not occur in freesurfer v6 even when using exactly the same data, but it does also occur with a d

Re: [Freesurfer] flirt.fsl error (NEWMAT::SingularException) when running bbregister in Freesurfer 7.0.0

External Email - Use Caution Hi Andrew, Thanks for looking into this. Yes, copying the binary from the v6 to the v7 installation does solve the issue. Julien ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

Re: [Freesurfer] flirt.fsl error (NEWMAT::SingularException) when running bbregister in Freesurfer 7.0.0

External Email - Use Caution Hi Andrew, I was just wondering whether this issue has been fixed in version 7.1.0? Thanks Julien ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

[Freesurfer] MGN and LGN in ThalamicNuclei segmentation

External Email - Use Caution Hello, I'm interested in locating the MGN and LGN using segmentationThalamicNuclei, but there is a mismatch between their location in the discrete segmentation (ThalamicNuclei.v10.T1.mgz) and the underlying  probability maps obtained by setting envi

Re: [Freesurfer] MGN and LGN in ThalamicNuclei segmentation

External Email - Use Caution Thanks Juan. Nevermind. It turns out that I was comparing a discrete segmentation done with v10 (Freesurfer v6 or older) with posterior probability maps obtained using v12 (Freesurfer 7.0) in the same subject. The locations of the MGN and LGN segmen

[Freesurfer] convert BA probability labels to volume

External Email - Use Caution Hello, I'm trying to convert label files containing probability values for Brodmann areas (e.g. rh.BA1_exvivo.label) to volume files using mri_label2vol. I'd like to keep the probability value that's in the 5th column of the label file into the vol

[Freesurfer] What exactly are the BA_exvivo.thresh label and annotation files?

External Email - Use Caution Hello, The ex-vivo BA label and annotation files named ?h.BA??_exvivo.thresh.label and BA_exvivo.thresh.annot seem to be thresholded versions of the corresponding probabilistic BA labels. Was a simple threshold on the probability used and if yes, wh