Hi Doug
I wanted to follow up this email and ask you a question. I see in the fspalm
page, it says "You can use fspalm with both volume- and surface-based analyses;
it will figure everything out".
Considering your reply to the below email, I'm wondering if we can use fspalm
for subcortical anal
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I'll note that we don't recommend trying to represent cortical areas in general
as single coordinates. We describe the issues with MNI space group average
volume alignment in this publication, which illustrates what happens to the
HCP's cortical area
I don't really know myself. This part runs a program from a 3rd party
-- the MNI (n3 bias field correction); we did not write it so it is
hard for us to debug. We often have problems with this program, so
unfortunately, it does not surprise me
On 9/19/19 12:42 PM, Lauricella, Michael wrote:
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Hi Doug,
Ok I'll verify the creation of the symlink today. Thank you for following-up.
Could you also maybe give me some details about what this termination status
means? : nu_correct: crashed while running nu_estimate_np_and_em (termination
status=
Hello,
I had emailed the Freesurfer Forum a few weeks back about trying the PALM
analysis for permutation testing. I recently tried fsPalm again on running some
of our subcortical analyses for the caudate, putamen, and nucleus accumbens,
and we performed the following steps:
* Set our res
What space are they in? Typically, I tell people to run recon-all on the
mni152 volume, then map labels into that subject, then compute coords
On 9/13/19 3:00 PM, Dev vasu wrote:
>
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> Dear all,
>
> I would like to obtain MNI coordinates for HCP annotations
There is not an easy way to do this. FS expects an intact whole brain,
and it tries to fit such into every brain, ie, it is trying to force a
whole cerebellum where there is none. What some people do is to fill the
lesion with "reasonable" intensities, eg, from the contralateral side.
Eg, you
You can run corrections for multiple comparisons (mri_glmfit-sim) to get
clusters of significant effects, then compute the mean over those clusters.
On 9/19/19 8:08 AM, AKUDJEDU, THEOPHILUS wrote:
>
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>
> Dear FreeSurfer,
>
> I used QDEC for the longitudinal
If you are getting negative values, it probably means that your model
(instantiated by the X matrix) is not proper in some ranges. The formula
below extrapolates the effects of the covariates in order to subtract
them off of a subject's value. If the model is not quite right, then the
extrapola
Not sure then. I've seen cases where the creation of symbolic links was
not possible on a cluster. It does not look like this is the problem,
but it could be doing something behind the scenes. Can you verify that
you can create a symlink from a program on the cluster? I've cc'ed Rob D
who can h
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Dear FreeSurfer,
I used QDEC for the longitudinal two‐stage model analyses, where temporal data
within each subject was reduced to a symmetrised percent rate of change (spc)
maps using the long_mris_slopes function for data acquired at two time-point
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