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
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
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#
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
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
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
>
>
>
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
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
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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
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
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
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
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
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