Dear experts,
For different reasons I found myself double checking the relationship
between t-values in t.nii and p-values stored in sig.nii. If I use the
following matlab code I thought that I should get the values of my_pval and
stored_pval to be the same (except perhaps for the sign):
cd(fullf
Hi Alexander,
Would it be possible to send me the volume file and one surface file
that has this shift problem?
Thanks,
Ruopeng
On 11/10/10 9:10 PM, Alexander Hunold wrote:
Dear experts,
I am perplexed how to fix the problem which is shown in the pictures.
The volume is the T1.mgz. The sur
Did you check the talairach.xfm? Can you send us the recon-all.log file?
On Nov 10, 2010, at 9:35 PM, "Joakim Vinberg" wrote:
> Sorry to add another!
>
>
>
> I ran recon-all on a subject of mine, and have recon-all exit with the error
> below. Based on the message, I examined both T1 and
Sorry to add another!
I ran recon-all on a subject of mine, and have recon-all exit with the
error below. Based on the message, I examined both T1 and nu.mgz. T1.mgz
is in fact totally empty-definitely not enough values of 110. Is this
due to a specific error that I might be able to bypass, or
my bet would be a bad tal xform, or maybe a bad skull strip. Which stage
was this one that failed?
On Wed, 10 Nov 2010, Nick Schmansky wrote:
> does the input image (T1.mgz) look ok? its possible to get as far as
> the skullstrip stage with garbage input (artifacts etc).
>
> n.
>
> On Wed, 2010-
does the input image (T1.mgz) look ok? its possible to get as far as
the skullstrip stage with garbage input (artifacts etc).
n.
On Wed, 2010-11-10 at 15:27 -0500, Rapuano, Kristina (NIH/NIMH) [F]
wrote:
> Hello again,
>
> As a new freesurfer-er, I have one more question: I have another recon-a
Hi Adam, your simulation is based on a whole-brain search space and so
it is not appropriate to use a label constraint when running
mri_surfcluster. If you want to constrain the correction of multiple
comparisons to a label, you have to do it when you do the simulation.
The best approach is act
I've done a little of this kind of thing, mostly tracking from thalamus
or amygdala to cortex, not starting at cortex, but the problem would be
the same. I have not had the problem that you describe, even when
starting at voxels clearly interior to thalamus (none of which is
actually labeled a
Hi, I had a question in reference to the following message (posted by Nick
Schmansky):
"1. in freesurfer v5, there are now multiple fsaverage subjects with
varying number of vertices. fsaverage6 has about 40,000 vertices per
hemi, so you can just include the flag:
--target fsaverage6
after th
Hi FreeSurfers,
I would like to use cortical surface ROIs generated in FreeSurfer to perform
inter-regional WM tractography using FSL's probtrackx tool. My understanding
is that start seeds and targest are typically defined by mapping the
labeled gray-white surface to the DTI volume. I.e., voxels
Hello again,
As a new freesurfer-er, I have one more question: I have another recon-all
script that failed during the skull stripping step. It says it exited with
errors, but does not actually specify any "ERROR" messages or even warnings.
This the last thing it runs before failing:
register_m
Hi FreeSurfers,
I would like to use cortical surface ROIs generated in FreeSurfer to perform
inter-regional WM tractography using FSL's probtrackx tool. My understanding
is that start seeds and targest are typically defined by mapping the
labeled gray-white surface to the DTI volume. I.e., voxels
Hi All,
We were wondering what is the best way to find the overlap of two label
files? For example, we want to save the region where segmentation1.label
and segmentation2.label files overlap.
Additionaly, we also wanted to know if we could find this region for the
overlap of three label files.
Hello,
I am fairly new to freesurfer, and recently encountered an error while running
recon-all (-autorecon1 -autorecon2) during Talairach Failure Detection:
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***Fp=0.0001, pv
Hi Elizabeth, I'm cc'ing the list so that others may benefit from the
answer:
The labels that you are referencing are defined in the aparc.a2009s
atlas, but the wmparc is generated from the aparc atlas. To generate a
wmparc using the a2009s, run the following:
cd $SUBJECTS_DIR/subject
mri_apa
Jacek,
i'm unable to replicate this problem using the data for the three
subjects that you sent me. -autorecon1 ran successfully and produced
good output for all three, both on a linux system and a mac. the
talairach stage did not segfault.
do you have enough disk space? do you have at least 2
Hi Freesurfers
I'm a bit confused as to some recent Monte Carlo findings I've been
looking at. After generating 10,000 estimations with mri_glmfit. I used
mri_surfcluster to generate nii, ocn.nii, and .sum files to analyze the
clusters. However I found that, when looking at the dACC, the cluster
w
I have no idea what is happening, but I can suggest a few checks. Have
you looked at the motion correction plots? Have you looked at the raw
data? Another thing to try is to turn off whitening when you make the
analysis for selxavg3-sess.
doug
Katie Bettencourt wrote:
> Hi all,
>
> I'm still t
Hi Elizabeth,
we'll need more info to track down the problem. Please take a look at
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for the kinds of things
we need.
thanks
doug
Elizabeth Gutierrez wrote:
> Hi,
>
> I've been trying to use mri_segstats on a FA map with a white matter
> parcellat
Hi,
I've been trying to use mri_segstats on a FA map with a white matter
parcellation file (wmparc.mgz) but there might be a problem in the program.
When I open the fa.stats output file, all the values (std.dev, etc) are
0. for the 2009 table parcellation ids. However, when I use the label
id
fyi, you can add the flag --cm to mri_nu_correct.mni to support hires
data. it will 'conform minimum' during mri_convert and not conform to
isotropic as is the default.
n.
On Wed, 2010-11-10 at 11:05 +0100, "Falk Lüsebrink" wrote:
> Hi Bruce,
>
> I'm so sorry, I should have double-checked. You
can you send me the 001.mgz file? i'll try to replicate. send to me
via:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
n.
On Tue, 2010-11-09 at 21:08 -0600, Freesurfer Local Archive wrote:
> Freesurfers,
>
> I am running freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 on a
> L
Hi Bruce,
I'm trying to process data with a higher native resolution than 1mm^3 in
order to investigate whether a better resolution leads to more accurate
results in terms of cortical thickness.
Best,
Falk Lüsebrink
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:
Hi Bruce,
I'm so sorry, I should have double-checked. You are completely right;
mri_normalize does work perfectly fine. The conformation to 1mm isotropic is
done in the last step of mri_nu_correct.mni.
In the last step of mri_nu_correct.mni the --conform flag is used, which
shouldn't be used:
Hi Falk,
can you give us a big picture of what you are trying to accomplish?
Bruce
On Wed,
10 Nov 2010, "Falk Lüsebrink" wrote:
Hi Bruce,
I'm so sorry, I should have double-checked. You are completely right;
mri_normalize does work perfectly fine. The conformation to 1mm isotropic is
done
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