Re: [Freesurfer] Total White matter and CSF value Calculation

Hi Douglas, Thanks for your support. From the below conclusion, can I say Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh + rh)Inf-Lat-Vent + (lh + rh)choroid-plexus + 3rd-Ventricle + 4th-Ventricle + 5th Ventricle + CSF. Also Is it correct t

[Freesurfer] white matter ROI mask using an fsaverage label

Hi Anastasia and FS experts, I am trying to create a white matter ROI mask underneath a cortical ROI label (e.g., 2 mm into the white matter) created in fsaverage space. I will then use this mask to extract values from individual dtifit_FA and dtifit_MD maps generated by trac-all. What would be

Re: [Freesurfer] Error: trac-all -prep "Segmentation fault (core dumped)"

Hi Walter – I’d check on the structural segmentation and its registration to the DWIs. Open dmri/dtifit_FA.nii.gz and label/diff/aparc+aseg.bbr.nii.gz and check if they’re well aligned and if the segmentation looks fine. On a separate note (and I don’t know if it’s related to the error you’re as

Re: [Freesurfer] Brain editing for TRACULA?

Hi Yuwen - TRACULA is pretty forgiving in terms of imperfections in the recon-all output. TRACULA uses only the aparc+aseg, after mapping it into the subject¹s diffusion space, which is typically lower-res than the structural. Also, TRACULA only uses the relative positions of white matter voxels to

Re: [Freesurfer] longitudinal TRACULA

Hi Lars – That’s correct, you don’t need to run cross-sectional TRACULA first, you just need to run longitudinal recon-all before you run longitudinal TRACULA, and it expects that the time points and base template subject IDs are the same for recon-all and for TRACULA. It sounds like the time po

[Freesurfer] Postdoctoral Fellowship at Harvard Medical School

Dear members, Please feel free to distribute the job ad below as you see fit. Best, Bengi Baran, Ph.D. Instructor in Psychiatry, Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging 149 13th Street, Room 2626 Charlestown Navy Yard Charlestown, MA 02129 em

Re: [Freesurfer] negative header after preproc-sess

Hi, Thanks for your reply, and I contacted with nibabel team based on your advice. They advice me to update my nibabel to the newest version, and now these data can be got properly:) Besides, I'm interested in the different dimension between `-surface self' and `-surface fsaverage`, they both

[Freesurfer] Volume based ROI projected to surface

Hi Freesurfers, I am doing a surfaced based ROI analysis on each of my subjects functional data. Using information from other papers, the size of the ROI really matters when doing the analysis, and I want to take this information from these papers and apply them to my own data. However, these

Re: [Freesurfer] niiRead error

It does work with 6.0, thank you! 2017-07-31 20:59 GMT+03:00 Douglas Greve : > I think this may be fixed in 6.0 > > On 7/31/17 12:43 PM, Francesca Strappini wrote: > > Thanks for the reply. > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. > > I opened it with fslview and it looks like a nor

Re: [Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

Thank you very much! :) Best Wishes, Elijah On 31 July 2017 at 15:37:38, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote: yes, mean across space. for vertex wise, you'll probably have to go into matlab, something like mask = MRIread('mask.mgh'); imask = find(mask.vol == 1); cc = MRIread('co