Re: [Freesurfer] propagating edits across in the FreeSurfer longitudinal stream

Hi Jessica, if you only have little changes across longitudinal time points, CP edits can be transferred from the base (instead of the cross runs) into specific longitudinal runs by specifying the -uselongbasectrlvol when running the -long. See https://surfer.nmr.mgh.harvard.edu/fswiki/Longit

[Freesurfer] Interpreting white matter regressor dat file

Hi, I have generated white matter regressor files for resting state analysis using fcseed-config and fcseed-sess. The resulting files include: wm.dat, wm.dat.pca-stats.dat and wm.dat.log. How do I interpret the wm.dat.pca-stats.dat file? There are 388 numbered rows (I'm guessing one per acquis

Re: [Freesurfer] recon-all issue

Hi Susanne can you include prior correspondance so we have some context for your emails. Certainly 2 vs. 1 and 3 will give different results since you have changed the input file. I would think think 1 and 3 would be the same, but we need to know how you did the conversion. Look at the 001.mg

[Freesurfer] registration errors in longitudinal analysis

Dear Freesurfer experts, I am working on a longitudinal analysis of cortical structure and am experiencing some errors with registration. I have 3 timepoints for each participant: time 1: age 2 time 2: age 5 time 3: age 10 Time 1 and 2 are from a 1.5T scanner. Time 3 is from a 3T scanner. De

Re: [Freesurfer] registration errors in longitudinal analysis

Hi Lara, the longitudinal pipeline is designed for adults with the assumption that head size is fixed. We are working on a new pipeline that will allow processing of images from children, but that will take a while. Especially considering that there will be large differences in the brain as w

[Freesurfer] Cortical thickness parcellates

Dear experts, I am wondering if there is any way to divide the cortical thickness parcellates in the atlas "?h.aparc.annot" by lobe. I highly appreciate any suggestion.   Bests, John  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

Re: [Freesurfer] Interpreting white matter regressor dat file

here you go (1) component number (2) variance spanned by that component (3) cumulative variance spanned up to that component (4) percent variance spanned by that component (5) cumulative percent variance spanned up to that component On 01/13/2016 09:56 AM, Afzal, Afsana wrote: > Hi

Re: [Freesurfer] Cortical thickness parcellates

Try mris_divide_parcellation On 01/13/2016 12:18 PM, John Anderson wrote: > Dear experts, > I am wondering if there is any way to divide the cortical thickness > parcellates in the atlas "?h.aparc.annot" by lobe. I highly appreciate > any suggestion. > > Bests, > John > > >

Re: [Freesurfer] Cortical thickness parcellates

Thanks Doug, I aim to create masks for the frontal lobe , parietal lobe, occipital lobe and temporal lobe including all the parcellates in every lobe in one maks. I was thinking to use mri_binarize but the number of the parcellates is very big. Is there a way that can give a direct maks for corti

Re: [Freesurfer] Cortical thickness parcellates

you can try mri_annotation2label with the --lobes or --lobesStrict option to see if that gets you where you need to be On 01/13/2016 12:49 PM, John Anderson wrote: > Thanks Doug, > I aim to create masks for the frontal lobe , parietal lobe, occipital > lobe and temporal lobe including all the pa

[Freesurfer] Longitudinal analysis_covariates

Dear Dr Martin, I have longitudinal database for subjects scanned multiple times. I want to study the changes in cortical thickness over time. I prepared my longitudinal table  ( column#1 fsid column#2 fsid-base column#3 group column#4 bilateral motor cortex thickness column#5 time (years) column#

Re: [Freesurfer] Trac-all -path Segmentation error

Hi Katherine - Do the freesurfer segmentations look ok? What about the registration from structural to diffusion? You can inspect those quickly with: freeview dmri/dtifit_FA.nii.gz dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.3 Hope this helps, a.y On Sun, 3 Jan 2016, Katherine

Re: [Freesurfer] X-inversion for b-vectors extracted via mri_convert?

Hi Emad - I wouldn't do tractography to check the gradient vectors. All you need is to look at are the principal eigenvectors of the tensors (dmri/dtifit_V1.nii.gz), displayed as lines (not just RGB map, that's less informative). If, for example, the z coordinates need to be inverted, then th