Hello!
My name is Achcha. I am a PhD student of Russian Medical Academy for
Postgraduate Education. In my research "Dementia with Lewy bodies" (DLB) I am
going to determine the association between the focal atrophy measures on MRI
and to compare it with clinical features of DLB. I try to
Dear FS Community,
I was wondering whether there is a way to create a binary volumetric file
of just the centroid of a binary volume (represented maybe as a dot of
1x1x1 mm^3 voxel size).
I know how to find the coordinates of the centroid (through either the
fslstats command or MATLAB), but I
what is your command? What is the terminal output?
On 01/22/2016 04:09 PM, AMY LIN wrote:
> Hi all,
>
> I'm trying to re-run subjects through recon-all for version 5.3.0 on a
> Mac 10.10.5 using Centos 6 but am not getting the normal output. There
> seems to be several strange things happening.
Dear FreeSurfer Team,
I am wondering how I can report Talairach coordinate and cluster size
(=surface area, mm^2) of the LME corrected results.
We can count the each clusters' number of vertices on fsaverage template by
checking the *.label. (is it right?) However, I don't know how we can the
Hi all,
I'm trying to re-run subjects through recon-all for version 5.3.0 on a Mac
10.10.5 using Centos 6 but am not getting the normal output. There seems to
be several strange things happening. The process ends almost
instantaneously and says that it finished without error, so I don't get any
Hi Amy
can you please send us the full command line and screen output? Otherwise
we can't help you.
thanks
Bruce
On Fri, 22 Jan 2016, AMY LIN wrote:
Hi all,
I'm trying to re-run subjects through recon-all for version 5.3.0 on a Mac
10.10.5 using Centos 6 but am not getting the normal
I just want to run plane correlation with the csf-variable
best
Eric
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The information in this e-mail is intended only for the person
Is this in regard to something you have posted before? If so, please
make sure to include previous correspondences. If not, please clarify
On 01/22/2016 01:05 PM, Erik Lindberg wrote:
> I just want to run plane correlation with the csf-variable
>
> best
> Eric
--
Douglas N. Greve, Ph.D.
I just want to investigate significant correlation with the csf variable
correcting for apoe-status, gender, diagnosis and age
below previous correspondence
your classes are right. What are you trying to test with your contrast
matrix?
On 01/20/2016 05:33 AM, Erik Lindberg wrote:
> Dear
Hi,
I studied the FreeSurfer code for MRISinflateBrain and came across a
discrepancy in how the sulcal depth is computed. This explains why the values
are much smaller than expected.
My question @Bruce is if this is intentional or (as the function names below
indicate) possibly a bug in the
Hello,
I am using mkanalysis-sess command to configure analysis and I have some
questions.
1, After run preproc-sess on raw data, why would we want to repeat all the
flag using for preprocessing at mkanalysis-sess (-stc up -fwhm 5). Is it
gonna effect to our f.nii if I input different value from
Hi Bruce,
I carefully followed your orientations. Kindly I still need more clarification regarding the following point:
I have statistical map in MNI152 space (volume) as an output of permutation analysis using " randomise/FSL". I want to visualize this map on an inflated surface in
It should take wild cards
On 1/21/16 8:16 PM, Luis Fernado Silva Castro de Araújo wrote:
Hi Freesurfer experts,
I wonder if there is a way of extracting the stats for all patients in
my last run at the same time. I have around 120 observations and the
asegstats2table syntax works in such a
Hi Daniel,
maybe you need to also install the tcsh package.
Best, Martin
On 01/21/2016 12:39 PM, Barron, Daniel wrote:
Hi List,
We just upgraded our Linux Box to Fedora 23 and installed csh so
recon-all would run, yet we’re still getting crashed analyses.
Here is the error from my
Maybe to avoid problems with strange subdirs (like fsaverage), use
|asegstats2table --subjects ??? \ --segno 11 17 18 \ --tablefile
aseg.vol.table|
if all subjects ids are three digits.
Best, Martin
On 01/22/2016 10:38 AM, Douglas Greve wrote:
It should take wild cards
On 1/21/16 8:16
Hi all,
I am loading a subject's surf (lh.pial) into MATLAB using read_surf(). At
the same time I have a mesh based on the original subject's anatomy in
.nii. The mm coordinates of these two do not match. Does anyone know why?
The same anatomy was used for surface reconstruction.
The very ranges
Hi Andreas
I just took a look at the code and it seems you are correct! Thanks for
catching this. I'll change the code base now and the fix will be in v6.
Bruce
On Fri, 22 Jan 2016, Andreas
Schuh wrote:
> Hi,
>
> I studied the FreeSurfer code for MRISinflateBrain and came across a
>
On 1/22/16 6:27 AM, John Anderson wrote:
Hi Bruce,
I carefully followed your orientations. Kindly I still need more
clarification regarding the following point:
I have statistical map in MNI152 space (volume) as an output of
permutation analysis using " randomise/FSL". I want to visualize
On 1/22/16 3:22 AM, Thục Trinh wrote:
Hello,
I am using mkanalysis-sess command to configure analysis and I have
some questions.
1, After run preproc-sess on raw data, why would we want to repeat all
the flag using for preprocessing at mkanalysis-sess (-stc up -fwhm 5).
Is it gonna
Dear Freesurfers,
I like to convert a cache.th13.abs.sig.cluster.mgh into a binary mask - so
that everything that is below 0.05 will be included in the mask - how can I
do this?
Eric
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what do you mean you have a mesh in the original subject's anatomy in
nii? Where did this come from? How was it created? If not from
FreeSurfer, then there is no reason to think that they coordinates would
line up. FreeSurfer uses its own (somewhat esoteric) coordinate system.
I would be
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