Hello,
I have been trying to run several versions of the same GLM analysis, trying
out different parameters to see if they affect the results. For instance, I
am running the GLM with different levels of smoothing, per-session versus
per-run motion correction, etc. To speed this up, I am trying to
Hello,
I am trying to run a retinotopy analysis in fsfast, using only polar angle.
However, when I try to run it, I am getting the error "Input to SVD must
not contain NaN or Inf." I have traced this error and it looks like the
design matrix X has 12 regressors (the first 12) that consist solely o
Hello,
I am trying to load five overlays on TKSurfer from the command line (actual
command attached). The problem is this: if I try to load five different
overlays, the fifth one will show up on Freesurfer as being identical to
the first one (for instance, in this example, the "all-slope" overlay
Hello,
I am thinking of switching from Tksurfer to Freeview, but I want to make
sure that retinotopy visualization still works well. Is it straightforward
to view phase-encoded displays? There are a few options on tksurfer
(complex color wheel, ability to set number of cycles and angle offset for
Hello,
I am looking to run a GLM on a single subject, where data was collected
across several different sessions. What is the best way to go about doing
this in the FSFAST pipeline? I was thinking that I should just 1) drop the
data for all the runs into a single BOLD directory as though they were
Hello,
I am getting an odd bug on selxavg3-sess. I am getting the error message,
*ERROR: cannot find [rest of file path]/fmc.sm0*
I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I am
confused because the output of preproc-sess for no smoothing is
fmc.nii.gz, *NOT
*fmc.sm0.nii.gz w
Hello,
Recently, I re-ran recon-all with Freesurfer version 5 on some subjects
whose surfaces had previously been reconstructed with Freesurfer version 4.
As a result, it appears that their surface reconstructions have subtly
changed, such that the labels that were specified in the old reconstruct
the surface from scratch?)
On Mon, Apr 10, 2017 at 5:46 PM, Taylor, Johnmark <
johnmarktay...@g.harvard.edu> wrote:
> Hello,
>
> Recently, I re-ran recon-all with Freesurfer version 5 on some subjects
> whose surfaces had previously been reconstructed with Freesurfer version 4.
Hello,
I had a quick question. Is there a way to make FSFAST output a 4D volume of
all the residuals? In other words: is there a way to see, for each voxel
and timepoint, how much of the BOLD response was unexplained by the GLM? I
know that it outputs a volume containing the residual variances, bu
Actually, just noticed that this is an option in selxavg3-sess, never mind!
On Wed, Jun 7, 2017 at 9:07 PM, Taylor, Johnmark <
johnmarktay...@g.harvard.edu> wrote:
> Hello,
>
> I had a quick question. Is there a way to make FSFAST output a 4D volume
> of all the residuals?
Hello,
Is there a simple way to retrieve the R^2 of the GLM model fit for each
voxel from the output of FSFAST? I wonder if rho1.nii.gz might be relevant,
but I couldn't find any documentation on this particular file.
Thank you very much,
JohnMark
___
Hello,
I am running into an odd issue. In particular, I have run a GLM analysis in
*volume* space, and I am visualizing the results both on the surface using
tksurfer, and on the volume using tkmedit. In both cases, I am using the
register.dof6.dat file to do the registration. Oddly, when I visual
Hello,
I am trying to do a GLM analysis for a study in which I scanned each
participant twice. Currently, to combine the two scanning sessions I am
combining the runs from the two sessions into a single session directory
and applying per-session motion correction, essentially treating all the
data
Hello,
Quick question. If I scanned a single subject across several sessions and
want to do a fixed effects analysis on that subject's brain (without
registering to MNI or Talairach space), how do I go about doing this? I am
trying to us isxconcat-sess and then mri_glmfit, but I am not seeing an
o
Hello,
A few quick questions about the "Per-Run" option in preproc-sess. I
understand that in this option, each run's images are registered to the
middle timepoint of that run, rather than the first timepoint of the first
run. I was wondering, though:
1) Why is this the preferred option instead o
: 2
> Date: Mon, 4 Dec 2017 12:32:00 -0500
> From: Douglas N Greve
> Subject: Re: [Freesurfer] Clarification about "Per-Run" Motion
> Correction and Registration in Preproc-Sess
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <813a5a08-d27e-a2a6-8472-66
Thanks once again for all the help on this. I am running the GLM in native
space, typically so that I can get the beta values to use in an MVPA
analysis. So it sounds like if you specify per-run motion-correction and
registration, and don't tell it to resample to anything (e.g., the MNI
brain or th
Hello,
When using preproc-sess and selxavg3-sess, how is global mean scaling
handled? Is the session-wide (4D) mean subtracted, is each volume's mean
subtracted, or neither?
Thank you very much,
JohnMark
___
Freesurfer mailing list
Freesurfer@nmr.mgh.h
Never mind, found the answer online, sorry about that!
On Mon, Dec 11, 2017 at 2:13 PM, Taylor, Johnmark <
johnmarktay...@g.harvard.edu> wrote:
> Hello,
>
> When using preproc-sess and selxavg3-sess, how is global mean scaling
> handled? Is the session-wide (4D) mean subtracted
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