This is the kind of thing that happens with clusterwise corrections. It
is hard to predict what happens. When you raise the threshold, you lose
some of the activation in your real map (ie, clusters become smaller).
But in the Null map, clusters also become smaller. So, at the lower
threshold, t
On 9/28/2023 4:13 PM, Lesage, Anne-Cecile wrote:
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Dear Freesurfer teams
I am working on sEEG data to help localize the epileptogenic zone at UTMB.
We were wondering with Dr Karas if we could use the *.inflated surface
to view better the electrodes in cont
If that is a volume label, then you will have to sample it on the
surface, eg, with mri_vol2surf. This will create a segmentation on the
surface (not a label). You can use vol2surf to map it all the way to
fsaverage, or you can map it on the native surface then use
mris_apply_reg or mri_surf2su
By default, mri_glmfit will "prune" voxels. Ie, if it finds any subject
that is zero at a given voxel, then that voxel is set to zero in the
output and in the mask. I suggest you load up your data
(lh.cbf.fsaverage.proj0.5sm00.nii.gz) as an overlay in freeview and
scroll through the subjects lo
On 9/27/2023 10:17 AM, Matteo Parodi wrote:
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Sure I try, thank you for the replay.
I'm using the above-mentioned analisis to obtain the Uptake for the
region in Desikan atlas, but the results are strange.
I think the error is in the last command but I'm
That is a bug in mri_compute_volume_fractions. That seg (29) has not
been given a tissue type. Probably there are like 5 voxels in there with
that label. In the short term, you can just replace it with another
label, eg 2 for left white matter or 41 for right white matter. You can
do this with
Yes, we have depricated the TclTk stuff. You should not have gotten that
error when using tkregisterfv. Can you send the command line and full
terminal output?
On 9/19/2023 7:02 PM, Nadvar, Negin wrote:
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Good afternoon,
I’m trying to run “tkregister2” in
yes, I think so too
On 9/19/2023 5:07 PM, gabriel robert wrote:
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Dear experts in longitudinal neuroimaging
We carefully read the papers about possible biases introduced by
treating timepoints images differently (Reuter and Fischl NI 2011, for
example) to
In general, I would recommend treating sex as a categorical rather than
continuous variable. To do this, you would have 6 groups (your 3 x 2
sex). I'm not sure what you are trying to test for. Eg, are you
interested in the difference between groups regressing out the effects
of age, DD, and sex
I doubt it. Have you tested it and found otherwise?
On 6/14/2023 3:23 PM, ruifen...@gmail.com wrote:
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Hi all,
I am running Freesurfer 7.3.2 on T1 images (LPI orientation) with
176*256*256 FOV, 1mm isotropic resolution.
I saw that the Ants N4 bias correct
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Just FYI, it is not intended that you process your
own subjects using SUBJECTS_DIR set to a path under where freesurfer is
installed, i.e., SUBJECTS_DIR in the log is set to,
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/recon-all
c
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