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> Dear Freesurfer expert
>
> I am trying to compute LGI with Mac OS. I am a beginner of FS.
> I could connect free surfer to Matlab path, but when I run LGI it generate
> this error that i can not understand
>
> mris_fill -c -r 1 lh.pial
> /Applic
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We had the same problem. This is related to a "security" feature Apple
introduced some years ago, called "System Integrity Protection".
Turn it off and you will be fine. Basically follow these instructions from
Apple:
https://developer.apple.com/
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Hi Freesurfers,
I'm trying to project the surface, a fine-grained parcellation
(?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it
is an annotation (NOT a surface) and an overlay. Use one of the surfaces
instead (e.g. lh.white)
cheers
Bruce
On Sun, 9 Dec 2018,
Winkelbeiner, Stephanie A wrote:
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Dear Martin,
actually, when your primary problem is very high local maxima on p-map, but no
significant cluster-wise p after thresholding, I guess, that you should try the
opposite, i.e. increase cluster forming threshold.
This will increase sensitiv
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Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform with
the lh.white surface?
Therefore, if I wanted to extract the mean FA f
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project
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Hello FS experts,
I was wondering if there is a command similar to annotval2surfoverlay.m
that allows converting subcortical values into aseg.annot subcortical
segmentation.
Thank you in advance and kind regards,
Lisbeth
_
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Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into
the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
