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 opt
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.
- mr
Dear FreeSurfer experts,
I am trying to use the LME toolbox to analyse the hippocampal change over
time in a group and also among 2 groups (2 scans per subject).
When I estimate the parameters with lme_fit_FS I become a warning saying
that the matrix is singular and my results are NaN. I guess th
pe2 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
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
> Dear Freesurfer experts,
>
> I have performed a VBM analysis with SPM, using some VOIs. Now I would
> like to compare the volumetric results o
Point in tksurfer. In tkmedit, Goto Saved Point, compare MNI305RAS to
> "MNI Coordinates". Note: 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 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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Dear Freesurfer experts,
How could I know the MNI coordinates of the 163.842 vertices of the left
hemisphere of fsaverage?
Best regards,
Yolanda
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305 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 fsaverag
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
"rh.thic
> Also I can 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 al
build 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
> H
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 = smooth(st,
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 f
tatistics is usually 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 ave
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 --thmi
you 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,
>>
>&
gt;
> 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 co
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
./fsaverage5/label/lh.
; that is specialized for transferring annotation files.
>
> --Thomas
>
> On Thu, Nov 24, 2011 at 4:11 PM, Yolanda Vives wrote:
> > Dear Freesurfer experts,
> >
> > I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations
> with my
> > dataset and I am
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 (rh.aparc.sp
, 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 wan
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
___
F
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
./fsaverage/mri/brainmask.mgz
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
$SUBJECTS_DIR/$subj/mri/aseg-i
second extracts 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
wavg space anyway? If you're going to just count voxels,
> it would be better to do it in the conformed space and not worry about what
> happens to the segmentation when you go do a lower res space.
>
> doug
>
> Yolanda Vives wrote:
>
>> Thank you Bruce!
>>
t 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
>
>
>
>
ommissures?
yolanda
2011/2/14 Douglas N Greve
> 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
>> obta
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. Afte
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 th
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
> Which coordinates are you using? Can you send me the label?
> doug
>
> Yolanda Vives wrote:
>
>> Hi Doug,
&
gt; 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 th
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 FS
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
I
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