Hello,
I wondering if possible using fsgd files to do group analysis with two
factors (one with 3 levels, one with 2 levels), with one covariate. On fsgd
example list I cannot find this example?
Kind Regards,
Linn
___
Freesurfer mailing list
Freesurfer
Hi FreeSurfers,
I ran the longitudinal processing pipeline on my subjects, FS 5.0.
Following the tutorial, first independently, then base, then long etc.
Everything works well, no problems there.
Out of curiosity I compared the asegstats & aparcstats within subject at
baseline (i.e. The same t
Hi list,
is it possible to create a ROI in an inflated surface within freeview or do
I have to use tksurfer?
It seems that I only can edit volume files.
After exploratory mri_glmfit, I want to outline a ROI in fsaverage inflated
surface and afterwards create a label to obtain CT averages per ever
Hi,
I understand that the recon-all script registers and then averages two
anatomical images (after bias field correction) if two are provided in the
"orig" folder, before performing the other parcellation stages. I am writing a
report and it might be good to mentioned what registration is used
Hi Wen,
Brain volume has a good relationship with the overall surface area measured
in native space (so, irrespective to any kind of interpolation). We found
an R^2 of 0.856, which is higher even than the correlation of brain volume
with gray matter volume as measured via VBM-like methods.
Howeve
Dear Eugenio,
Thanks for the reply. Yes, we created a test directory containing two subjects
that have been reconed with the -hippo-subfields flag. Both of them have 20
output files.
Cheers,
Zoe
From: Juan Eugenio Iglesias [mailto:igles...@nmr.mgh.harvard.edu]
Sent: Monday, June 24, 2013 5:03 P
What was the exact call? Did you try setting SUBJECTS_DIR to the
directory at hand and running the command without arguments?
Cheers,
/Eugenio
On 06/25/2013 09:06 AM, Yang, Zoe wrote:
Dear Eugenio,
Thanks for the reply. Yes, we created a test directory containing two
subjects that have been
Hi All,
I'm running Monte Carlo simulations on functional data, and the coordinate
information outputted in the cluster.summary file isn't making sense. Usually
the coordinates for the clusters listed are Talairach coordinates, but in the
.summary files I'm getting, the coordinates are labeled
Dear, Zoe
Usually after Freesurfer fresh install you will get a SUBJECTS_DIR with
several directories, including Bert. The script you used will scan all
directories under SUBJECTS_DIR and if it finds any directory without the
posterior*.mgz files it will fail. You can check if this is the problem
r
Dear experts,
I'm new to CUDA. I tried to use CUDA in my environment, it gives the
message below:
Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221
Driver
Doug - thanks that sounds well worth trying.
the labels we have have arbitrary spatial resolution in the saggital plane,
and 1mm gaps between saggital slices.
In general in this project we are using an isotropic resolution of 0.25mm.
To generate surfaces in freesurfer I have to downsample to 0.3
yes, it's rigid and used to be sum of squares but in the newer versions we
will be using Martin's robust registration (which is a tukey biweight
instead of SSE)
On Tue, 25 Jun 2013, Parker, Christopher wrote:
> Hi,
> I understand that the recon-all script registers and then averages two
> anato
can you send the file?
On 06/25/2013 10:08 AM, Emily Boeke wrote:
> Hi All,
>
> I'm running Monte Carlo simulations on functional data, and the coordinate
> information outputted in the cluster.summary file isn't making sense. Usually
> the coordinates for the clusters listed are Talairach coord
On 06/25/2013 12:12 PM, Colin Reveley wrote:
> Doug - thanks that sounds well worth trying.
>
> the labels we have have arbitrary spatial resolution in the saggital
> plane, and 1mm gaps between saggital slices.
>
> In general in this project we are using an isotropic resolution of 0.25mm.
>
> To
Hi Linn, yes it is possible. It just requires 6=3x2 classes. Can you
generalize from the 2 factors/2 levels cases?
doug
On 06/25/2013 03:39 AM, Linn Mittlestein wrote:
> Hello,
>
> I wondering if possible using fsgd files to do group analysis with two
> factors (one with 3 levels, one with 2 l
Hi Chris,
we actually do use my robust registration tool for it since a while (FS
5.0, Aug 2010), replacing FLIRT which was used before. Here is the citation:
M. Reuter, H.D. Rosas, B. Fischl. *Highly Accurate Inverse Consistent
Registration: A Robust Approach*. /NeuroImage 53(4):1181-1196, 2
Hi Cedric,
this is as expected, the data changes when using the longitudinal stream
(it will become more reliable, removing some of the variance you get in
the independent processing). Becuase of the different processing
approaches, the results from independent processing (cross) and long
wil
Hi Sandra,
is the environment variable SUBJECTS_DIR setup correctly ? in newer
versions of the script this needs to be passed on the command line, but
in 5.1 I think it needs to be set as an evironment variable.
Best, Martin
On 06/21/2013 04:35 AM, Sandra Preissler wrote:
> Dear freesurfer us
Hi there,
I'm wondering if there's any parameter which can assess the correctness of
the freesurfer's segmentation ( the aparc.a2009s+aseg.mgz file).
--> Assuming the freesurfer's algorithm fitting/minimizing an objective
function, right ? If so, where I can find the value of this fitted functio
On Tue, Jun 25, 2013 at 10:55 AM, Clive Wong wrote:
> I'm new to CUDA. I tried to use CUDA in my environment, it gives the message
> below:
>
> Testing for CUDA device:
> nvcc: NVIDIA (R) Cuda compiler driver
> Copyright (c) 2005-2012 NVIDIA Corporation
> Built on Fri_Sep_21_17:28:58_PDT_2012
> C
Hi Dov
I think it writes out the log posterior at each iteration of the aseg
(mri_ca_label)
cheers
Bruce
On Tue, 25 Jun 2013, Dov Sadan wrote:
Hi there,
I'm wondering if there's any parameter which can assess the correctness of
the freesurfer's segmentation ( the aparc.a2009s+aseg.mgz file)
Hi again,
Zoe, Marcos is right about the fact that the script fails if the
posterior*.mgz are not found in any
1- Set your $SUBJECTS_DIR variable as another another path and move
your subjects directories (and only these directories to this place)
and run the same script you tried
(kvlQuanti
Dear Buche,
Thank you very much for your quick reply.
Do you mean those lines: (from recon-all. log)
==
.
.
.
gca peak = 0.27536 (62)
mri peak = 0.11940 (97)
Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, overlap=0.
000)
Right_Hippocampus (53): linear fit = 1.55 x
oops :) Bruce
On Tue, Jun 25, 2013 at 10:32 PM, Dov Sadan wrote:
> Dear Buche,
>
> Thank you very much for your quick reply.
>
> Do you mean those lines: (from recon-all. log)
> ==
> .
> .
> .
> gca peak = 0.27536 (62)
> mri peak = 0.11940 (97)
> Right_Hippocampus (53): linear f
No, not that. That is the density reestimation. Later on it should write out
the log posterior
On Jun 25, 2013, at 3:32 PM, Dov Sadan wrote:
> Dear Buche,
>
> Thank you very much for your quick reply.
>
> Do you mean those lines: (from recon-all. log)
> ==
> .
> .
> .
> gca
for the aseg it's these lines:
.
.
.
pass 1: 89966 changed. image ll: -2.224, PF=1.000
pass 2: 15019 changed. image ll: -2.221, PF=1.000
pass 3: 5116 changed.
pass 4: 2124 changed.
writing labeled volume to aseg.auto_noCCseg.mgz...
although I guess I only compute it for the first couple of iterat
"LL" stand for *L*og*L*ikelihood ? ;-)
On Tue, Jun 25, 2013 at 10:57 PM, Bruce Fischl
wrote:
> for the aseg it's these lines:
> .
> .
> .
> pass 1: 89966 changed. image ll: -2.224, PF=1.000
> pass 2: 15019 changed. image ll: -2.221, PF=1.000
> pass 3: 5116 cha
Yes, although I think it's actually the log posterior
On Jun 25, 2013, at 4:01 PM, Dov Sadan wrote:
> "LL" stand for LogLikelihood ? ;-)
>
>
> On Tue, Jun 25, 2013 at 10:57 PM, Bruce Fischl
> wrote:
> for the aseg it's these lines:
> .
> .
> .
> pass 1: 89966 changed. image ll: -2.224, PF=
Hi Martin,
Thanks for your fast response. Apologies for the second email, I forgot to
include the mailinglist.
It makes sense that in the longi-stream results should be more reliable.
However, it worries me if I see segmentation differences up to 500%, for
example amygdala volume going from 14
Hello again,
I also tried the command line options. I get an error for ill-conditioned
matrix. Could it be because of possible correlations between covariates? For
example I am using Age and mean thickness, should I just use one of them?
Here is the error:
wrls-guest-166-198:subjects manishd
Hi,
I am examining the affect a metal artifact has on fMRI data, and I am
using Eccentricity mapping with the retinotopy analysis in FSFast. I
was recently asked to switch from examining the difference in the fsig
to examining the difference in the betas. I opened up beta.nii.gz and
I can see that
Hi All,
I'm having a problem related to that of Ed Gronensch (see below) with viewing
the hippocampal subfields overlaid on the nu.mgz mri in Freeview. I recently
installed the most recent version for FreeSurfer (lion for MAC). When I use the
command listed on the website ( cd $SUBJECTS_DIR/be
Hi Sal
can you cat that file and email us the contents? Sounds like it got
messed up
Bruce
On Tue, 25 Jun 2013, Salil Soman wrote:
> Dear Freesurfer experts,
>
> I had been running freesurfer 5.3 without trouble on a sungrid cluster of
> ubuntu servers. Recently, however, I am now getting a new
33 matches
Mail list logo
