is larger, if positive slope1 is larger. Note that
if your slopes are negative, e.g. atrophy, then larger means closer to zero
= less atrophy.
Best, Martin
On 05/28/2013 11:57 AM, Yolanda Vives wrote:
Dear FreeSurfer experts,
I am trying to use the LME toolbox to analyse the hippocampal
Dear FreeSurfer experts,
I am performing a DODS analysis with QDEC to compare cortical thickness of
patients and controls and I have some questions regarding the nuisance
factors age and global cortical thickness.
1.- Should I demean both variables or only the age?
2.- Which of the following
Dear FreeSurfer experts,
I would like to know the area of some manually drawn labels, obtained with
QDEC over fsaverage. I have used the following scripts, but I had errors in
both of them.
- label_area. It doesn't work because it requires surf/lh.smoothwm, which
is not present in fsaverage.
-
Dear Freesurfer experts,
I have performed a VBM analysis with SPM, using some VOIs. Now I would like
to compare the volumetric results obtained with SPM with those of cortical
thickness obtained with Freesurfer in the same VOIs (approximately).
For this purpose, I would like to transform the MNI
Dear Freesurfer experts,
How can I transform from MNI coordinates to RAS surface coordinates?
Regards,
Yolanda
2012/6/5 Yolanda Vives yvi...@pic.es
Dear Freesurfer experts,
I have performed a VBM analysis with SPM, using some VOIs. Now I would
like to compare the volumetric results
: you may need to use the Volume RAS from
tkmedit in the computation above to get an exact match.
On 06/06/2012 09:43 AM, Yolanda Vives wrote:
Dear Freesurfer experts,
How can I transform from MNI coordinates to RAS surface coordinates?
Regards,
Yolanda
2012/6/5 Yolanda Vives yvi
Dear Freesurfer experts,
How could I overlay spmT.img maps from a VBM study on fsaverage? I would
like to convert the significant clusters into labels.
Thank you in advance,
Yolanda
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Freesurfer@nmr.mgh.harvard.edu
Dear Freesurfer experts,
How could I know the MNI coordinates of the 163.842 vertices of the left
hemisphere of fsaverage?
Best regards,
Yolanda
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
, the coordinates are the MNI305 coordinates.
doug
On 06/19/2012 08:48 AM, Yolanda Vives wrote:
Dear Freesurfer experts,
How could I know the MNI coordinates of the 163.842 vertices of the
left hemisphere of fsaverage?
Best regards,
Yolanda
Hi Martin,
I would like to compare also a Control vs. an Experimental group
(pre-post), but instead of using ROIs, I am interested in a whole-brain
paired t-test analysis between the two groups. Which data should I take?
Would it be possible to process ?.long.base with qcache and take the
make available a newer version of that script as lots of
small things have changed since last year, let me know.
Best, Martin
On Tue, 2012-07-03 at 15:58 +0200, Yolanda Vives wrote:
Hi Martin,
I would like to compare also a Control vs. an Experimental group
(pre-post), but instead
this
cross table from my long table?
Exemple of my longitudinal table:
fsidfsid-base group
preJMS_007JMS_007 ON
postJMS_007 JMS_007 OFF
preRME_063 RME_063 ON
postRME_063 RME_063 OFF
...
Thank you very much,
yolanda
2012/7/4 Yolanda Vives yvi...@pic.es
Dear all
I am a new user of the LME matlab toolbox and I have an error when
running lme_lowessPlot due to the smooth function. Do I need a
particular matlab toolbox to run this function? I have not seen any
smooth function in the LME toolbox.
Error in == lme_lowessPlot at 49
ybw =
Dear FreeSurfer experts,
I have run a longitudinal study considering multiple time points (7
scans/subject on average) with FS 5.1. However, I am interested in the
percent changes between two time points only (between 0 and 6 months
and between 0 and 1 year). Should I run the longitudinal stream
a bad idea as you
loose power.
Best, Martin
On 03/18/2013 01:15 PM, Yolanda Vives wrote:
Dear FreeSurfer experts,
I have run a longitudinal study considering multiple time points (7
scans/subject on average) with FS 5.1. However, I am interested in the
percent changes between two time
Dear freesurfers,
I would like to obtain the cluster size (in mm3) and coordinates of the
maxima of a cortical volume comparison using mri_surfcluster.
mri_surfcluster --in
$PATH/control_cronic_dones_right_volume/rh-Diff-control-cronic-Intercept-volume/sig.mgh
--hemi rh --subject fsaverage
want I assume). That command otherwise looks right, but it won't
correct for multiple comparisons. You can run mris_anatomical_stats on the
output label to give you the stats you want.
doug
Yolanda Vives wrote:
Dear freesurfers,
I would like to obtain the cluster size (in mm3
it.
cheers
Bruce
On Thu, 28 Jul 2011, Yolanda Vives wrote:
Thank you Douglas for your suggestions!
If I use mris_anatomical_stats, would I perform the following procedure?
- To run mri_label2label to all the subjects of my comparison
- To run mris_anatomical_stats. I would obtain the volume
Dear Freesurfer experts,
I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations with
my dataset and I am not sure what I have to do. I have used the
mris_annot_to_segmentation command but I have the following error:
mris_annot_to_segmentation BASGU lh inflated
.
--Thomas
On Thu, Nov 24, 2011 at 4:11 PM, Yolanda Vives yvi...@pic.es wrote:
Dear Freesurfer experts,
I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations
with my
dataset and I am not sure what I have to do. I have used the
mris_annot_to_segmentation command but I have
Dear Freesurfer experts,
I have a question regarding mris_divide_parcellation. I have created a file
containing the parcels from aparc.annot that I want to split and I have run
the following command. Why is Freesurfer allocating 36 additional units?
When I open the new annotation file
, unused color
table entries)
Bruce
On Tue, 7 Feb 2012, Yolanda Vives wrote:
Dear Freesurfer experts,
I have a question regarding mris_divide_parcellation. I have created a
file containing the parcels from aparc.annot that I want to split and I
have run the
following command. Why
Dear Freesurfer experts,
In Freesurfer v5.1, aseg.stats files give the value of total gray matter
volume. Is this label in the annotation file? How can I know which voxels
from the brain are considered as gray matter?
Thank you in advance,
Yolanda
___
Dear Freesurfer experts,
I would like to transform the aparc.annot file into MNI space in order to
map the parcels from this file to the MNI152_T1_1mm atlas. I have tried the
following unsuccessfully:
./mri_label2vol --annot lh.aparc.annot --subject fsaverage --temp
Hi all,
I have read about the eTIV and how to obtain it in the paper from Buckner
et al. but I have a question related to the implementation of it in
Freesurfer, just to be sure that I have correctly understood it. Regarding
the volumes of the subcortical structures presented in aseg.stats, are
Hi all,
We have a problem with Freesurfer v4.3.1. The output files
lh.aparc.stat/rh.aparc.stat don't contain the results corpuscallosum
(there are only 35 entries in the file and corpuscallosum is missing). Is it
a known bug?
Thank you for your time,
Yolanda
Dear freesurfer's,
I have run a conventional recon-all process and I am interested in isolating
the caudate from my subjects. I have applied the following commands:
*./mri_label2vol --seg $SUBJECTS_DIR/$subj/mri/aseg.mgz --temp
$SUBJECTS_DIR/$subj/mri/rawavg.mgz --o
the caudate from
that volume. If you want the caudate in the conformed space, just use
aseg.mgz in the mri_extract_label command instead of aseg-in-rawavg.mgz
cheers
Bruce
On Thu, 10 Feb 2011, Yolanda Vives wrote:
Dear freesurfer's,
I have run a conventional recon-all process and I am
...@nmr.mgh.harvard.edu
not if you just want to compare volumes. If you want to compute overlap it
would be, but note that you'll probably be biased towards lower overlap as
you will induce some sampling errors mapping the aseg to the original voxel
space.
cheers
Bruce
On Mon, 14 Feb 2011, Yolanda Vives
?
yolanda
2011/2/14 Douglas N Greve gr...@nmr.mgh.harvard.edu
yes, it is.
doug
Yolanda Vives wrote:
Hi Doug,
I am interested in coming back to rawavg space because we have the
caudates segmented manually and we would like to compare the volumes
obtained automatically with those obtained
Hi all,
I am interested in obtaining the MNI or talairach coordinates of a label.
The procedure that I have performed is the following:
First of all I have performed a QDEC analysis. From the results, I have
drawn a label of a significant area of the brain, that corresponds to the
cingulate.
, they should already be in mni305 coordinates, so the identity
matrix is correct. Did you find a potential problem?
doug
Yolanda Vives wrote:
Hi all,
I am interested in obtaining the MNI or talairach coordinates of a label.
The procedure that I have performed is the following:
First
I am using the coordinates obtained with the matlab function read_label().
I send you one of my labels.
Thanks a lot,
Yolanda
2011/5/3 Douglas N Greve gr...@nmr.mgh.harvard.edu
Which coordinates are you using? Can you send me the label?
doug
Yolanda Vives wrote:
Hi Doug,
The problem
the right
hemisphere? The first coordinate of all the points is negative, indicating
that it is on the left side. Which MNI atlas are you using?
doug
7705 -36.725 5.727 20.658 0.00
Yolanda Vives wrote:
I am using the coordinates obtained with the matlab function
read_label(). I send
Dear Freesurfers,
I have a dataset processed with a classical recon-all of Freesurfer v.4.3.1
and there are two MRIs that were not segmented correctly due to the
register. After several unsuccessful attempts to improve this step using
tkregister2, finally I have successfully processed them with
External Email - Use Caution
Dear Samseg developers,
I have very high resolution T1 (512 x 512 x 240; voxel size: 0.469 x 0.469
x 1) and FLAIR images ( 384 x 384 x 128; voxel size: 0.495 x 0.495 x 1) and
I would like to process them with the longitudinal processing of samseg but
36 matches
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