POST DOCTORAL POSITION in BORDEAUX
The Neurofunctional Imaging Group (GIN) is a CNRS-CEA joint research unit of
the Bordeaux University (UMR 5296, dir.
Bernard Mazoyer) and a core member of the TRAIL Laboratory of Excellence. The
GIN is a multidisciplinary research unit
gathering scientists
Hi Emma,
Please, see below:
On 13 October 2014 20:11, Emma Thompson vonecono...@gmail.com wrote:
Hi Anderson,
Thank you for your paper. I guess I am confused. I have analyzed my
structural data with qdec, specifically looking at a measure of cortical
thickness and volume. I'm considering
Hi Kate
so something is going wrong with the MNI NU correct tool. Maybe someone on
the FS list knows how to fix this, but if not you might want to check with
the MNI people
cheers
Bruce
On Tue, 14 Oct
2014, Kate Riggall wrote:
Hi Bruce,
The output is as follows:
Hi Knut,
the longitudinal stream assumes head size is fixed across time. That is
why we report only one ICV (the one from the within subject template) in
all time points. If in your data heads are growing still, you can still
use the longitudinal stream, but need to be carefully inspecting
If you are using --qcache, then there is nothing wrong specifically with
the qdec implementation
On 10/13/2014 03:11 PM, Emma Thompson wrote:
Hi Anderson,
Thank you for your paper. I guess I am confused. I have analyzed my
structural data with qdec, specifically looking at a measure of
Which cortical thickness measure? The value in the stats file or the
values in the map prior to voxel-wise analysis?
On 10/10/2014 03:57 AM, Adam, Ruth wrote:
Hi,
I would like to exclude areas which were incorrectly segmented and
could not be corrected after editing and re-running
That call to aparcstats2table will give you the surface area. Use -m
thickness. With this, it will report whatever you passed as the -t
option to mris_anatomical_stats (rh.pial_lgi in this case).
doug
On 10/13/2014 07:49 AM, elisa veronese wrote:
Dear FreeSurfers,
I'm facing a problem
Hi,Would that make a difference?I would like to use the stats file, unless you recommend otherwise. Thanks!Best,ruthiOn 14 Oct 2014, at 17:43, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:Which cortical thickness measure? The value in the stats file or thevalues in the map prior to voxel-wise
They are different analyses. If you want to use the stats file, then
you'll need to edit the parcellation/annotation to remove the offending
areas. I think you can do this in FreeView, but someone else will have
to guide you because I've never done it.
doug
On 10/14/2014 11:57 AM, Adam,
Yes, there is, and there is an adjustment made to the vox2ras so that
freeview reads it properly. Still that should not affect the actual
coordinates. However, if you want to use another viewer, you have to
make sure that the coordinates are consistent between the volume and the
surface. Just
Dear experts,
Can one use mri_anatomical_stats to extract volume information? I have a
set of labels that has been mapped to each subject's native space (using
mri_label2label; the original labels were extracted from group comparisons
using mri_glmfit).
I have successfully extracted the
Hello all,
I am wanting to put labels currently in diffusion space into MNI space.
Does this make sense or is there a more straight forward way?
1. mni152reg the subject's structural into MNI space
2. inverse transform the MNI in the the subject's T1 space
3. Use bbregister to align the DTI to
Hi All,
I'm trying to extract signal from an ROI in an analysis that I specified
as FIR. Using funcroi-config and funcroi-table-sess, I'm able to produce
an output file that gives me a single value for each participant. What
I'm trying to do is to get a value for each TR in the time window I
It is still possible but not quite as easy. You have to create a
contrast for each tap in the FIR, then run funcroi for each tap.
doug
On 10/14/14 7:02 PM, Joseph Andreano wrote:
Hi All,
I'm trying to extract signal from an ROI in an analysis that I specified
as FIR. Using funcroi-config
Use -t hemi.volume (and change the name of the output file:-)
doug
On 10/14/14 2:30 PM, Vy Dinh wrote:
Dear experts,
Can one use mri_anatomical_stats to extract volume information? I have
a set of labels that has been mapped to each subject's native space
(using mri_label2label; the
Hi Joe,
I assume that you have already 1) defined your FIR function
(mkanalysis-sess) and applied it (selxavg3-sess). I also assume that you
have already defined your ROIs (funcroi-config) and applied them
(funcroi-sess). Up to this point, everything is more or less easy. Now,
you want to
Hi Corinna, once you do #1, you can concatenate the register.dat with
the mni152.2mm.reg.dat like this
mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
Check
tkregister2 --mov dti.nii --targ
$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
mri_vol2vol --mov
Hi Dr. Greve,
I'm encountering a segmentation fault for some subjects when I run the
following command:
mris_anatomical_stats -l $label -t $hemi.volume -b -f $sublabel $sub $hemi
*This is the program output for a subject that had the segmentation fault.
Strangly, this occurs with the volume
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