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Hello Peter,
This thread was made 3 months ago, but I post additional information here. Hope
it will help anyone who meets the same issue.
My environment is almost same as yours (FS ver. 7.1 on macOS Mojave), and I
experienced the same error.
Versio
Hi Georgia,
I think you forgot to run the last word "fs_install_mcr" in that command (after
chmod +x). That’s why chmod is throwing a usage error. That doesn’t solve the
reason why it’s not downloading though. Can you try a different tool, like wget
and let me know if anything downloaded:
wget
Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you installed
minc tools separately on your local machine and do you have any of these
variables set in your default environment?
MNI_DIR
MINC_BIN_DIR
MINC_LIB_DIR
It’s possible there’s another install of MNI that’s interfering wi
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Hi All
As a frequent user of minctools, I know I’ve had problems in the past if I
source minctools before sourcing freesurfer in the same terminal, because
freesurfer uses an older version of minctools.
Also, freesurfer uses minc1 format not minc2.
Use mris_anatomical_stats to create an LUT with the -c option. You can
look in recon-all.cmd for an example. You only need to do one hemi as
they both will be the same.
There are four sections of the new LUT: lh cortex, rh cortex, lh WM, and
rh WM. For each one, you replicate the LUT created abo
In principle, yes. But, the atlas was trained using MS, not AD-style,
lesion data, and some recent analyses has shown the segmentation to be
hit-or-miss on leukoaraiosis-like data. Git it a try and give us feedback.
On 2/9/2021 12:15 PM, Steve Petersen wrote:
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Dear Freesurfer experts,I'm using the LME model for longitudinal study
and I'm running the part of parameter estimation but MATLAB "told me"
than the file "libgeodesic.so" is not available or does not exist. So
check in FreeSurfer' folder and it's not t
Hi there,
First, I ran "mri_glmfit" using a mask (subcortical regions) as follows:
mri_glmfit --glmdir g1v1.wls --y ces.nii.gz --wis cesvar.nii.gz --fsgd
g1v1.fsgd --C age.mtx --mask brain.mni305.2mm.nii.gz --fwhm 5.
Second, I'm going to process "mri_glmfit-sim" to perform a cluster-wise
correc
