I would like to raise it again before it's completely forgotten.
At the meantime I keep receiving Emails from people asking me this issue.
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 3/19/13 7:07 AM, Yang
.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter SpeedComm Telecom
-- www.netfilter.com.brhttp://www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
, Apr 10, 2013 at 12:04 PM, Yang, Daniel
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:
Hi PPJ,
Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any
chance you could also provide the cortical thickness of the 2009 atlas (e.g.,
rh)?
I will take a look
gm
voxels, as those are not accurate (ie, dont load aseg.mgz when
inspecting surfaces, or at least turn if off when inspecting gm
regionsits still handy to see where hippocampus sits).
Nick
On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote:
Dear FreeSurfer Experts and Users,
Did
On 4/16/13 10:44 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
glad to hear it
Bruce
On Tue, 16 Apr 2013, Yang, Daniel wrote:
Thanks so much for the improvement!
I ran the new mris_make_surfaces and the pial surfaces look much better
in
FS 5.2!
Here is the comparison slice if you're
Dear FreeSurfer Experts and Users,
This is probably a basic question, so please bear with me.
I'm looking at the Coronal view in tkmedit, and I am wondering how does
FreeSurfer knows where a gyrus ends and a sulcus begins (and vice versa).
For example, I'm looking at the superior temporal
is usually deemed to be
cheers
Bruce
On Mon, 22 Apr 2013, Yang, Daniel wrote:
Dear FreeSurfer Experts and Users,
This is probably a basic question, so please bear with me.
I'm looking at the Coronal view in tkmedit, and I am wondering how does
FreeSurfer knows where a gyrus ends and a sulcus
Dear all,
in the aseg.volume, there is a term called 'ventral DC' and I am wondering what
it is.
I looked up the previous posts and know DC = diencephalon, and it's a grab bag
of stuff that cannot be resolved.
However, does anyone know what exactly ventral DC is?
Thanks!
Daniel
--
Yung-Jui
...@nmr.mgh.harvard.edu wrote:
Hi Daniel
it's a bunch of things like substancia nigra, the subthalamic nucleus,
LGN (I think), etc
Bruce
On Fri, 31 May 2013, Yang, Daniel wrote:
Dear all,
in the aseg.volume, there is a term called 'ventral DC' and I am wondering
what it is.
I looked up the previous posts
Hi FreeSurfer expert,
I am interested in a particular region of the Desikan-Killiany atlas and I'd
like to use it as an ROI image mask in my fMRI analysis.
Could you please suggest how I can do that?
From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), I see
that the DK
Dear FreeSurfer Expert,
I would like to draw the specific ROI of the DK atlas (not specific individual,
but this ROI in general). I'm wondering how this ROI can be extracted/created
as a mask so that I can draw it on the brain using some software?
Could you please advise?
Thanks a lot,
Daniel
2013,
Yang, Daniel wrote:
Dear FreeSurfer Expert,
I would like to draw the specific ROI of the DK atlas (not specific
individual, but this ROI in general). I'm wondering how this ROI can be
extracted/created as a mask so that I can draw it on the brain using some
software?
Could you please advise
).
cheers
Bruce
On Tue, 16 Jul 2013, Yang, Daniel wrote:
Hi Bruce,
I am sorry, I mean, is there a DK atlas on a standard template brain (like
MNI 152)? sorry, I don't know how DK atlas works. Is it a probabilistic
atlas, or dependent on the exact folding pattern of the unique individual?
(I guess
instruction? In freeview,
I found that I can only load ROI after I load a volume, but not after I load a
surface.
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 7/16/13 10:14 AM, Yang, Daniel
yung-jui.y
lh.inflated:label=lh.your_ROI.label
cheers
Bruce
On Tue, 16 Jul 2013, Yang, Daniel
wrote:
Hi Bruce,
Sorry for so many responses. I figured it out that I can visualize it using
tksurfer.
Besides this, can I visualize it in freeview, CARET, or some other tools? My
goal is to display the ROI on a fsaverage
Dear FreeSurfer Experts,
I am interested in a specific ROI in the DK atlas, and I know that I can use
tkregister2 to obtain a register.dat, and then mri_annotation2label +
mri_label2vol to convert the annotation of the ROI to an .nii.gz.
However, it seems that the end product is in the TAL
Hi Doug,
Thanks very much!!
Best,
Daniel
On Jul 16, 2013, at 9:14 PM, Douglas Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
use
$FREESURFER_HOME/average/mni152.register.dat
doug
On 7/16/13 8:36 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
I am interested
Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 7/16/13 9:13 PM, Douglas Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
use
$FREESURFER_HOME/average/mni152.register.dat
doug
On 7/16/13 8:36 PM, Yang, Daniel wrote:
Dear
Hi FreeSurfer Expert,
So GFEAT results are in MNI152 standard space. Is there a way I can visualize
the GFEAT results on a fsaverage surface?
For example, if I do the following, would that be okay?
tksurfer fsaverage lh inflated -annot aparc.annot \
-ov
statistical maps onto a
fsaverage surface
That won't work. If you are going to use anat2std.register.dat, then you will
need to specify the individual subject instead of fsaverage. For fsaverage, use
$FREESURFER_HOME/average/mni152.register.dat
doug
On 8/1/13 7:11 PM, Yang, Daniel wrote:
Hi FreeSurfer
Hi FreeSurer Expert,
I am wondering if there is a way that the annotation can be made somewhat
transparent in freeview so that I can still see the functional activation on
top of the annotation?
Thanks,
Daniel
___
Freesurfer mailing list
Dear FreeSurfer Experts,
I'm looking at stats/wmparc.stats, and there are some inconsistencies between
subjects. I am wondering what might be the cause.
For one subject (say subject 1), part of the information appears to be:
# NRows 66
# NTableCols 10
# ColHeaders Index SegId NVoxels
Dear FreeSurfer Experts,
Theoretically, if you have a set of functional ROIs, is it possible to derive
the cortical thickness, white surface area, and gray matter volume of those
functional ROIs in FreeSurfer?
Many thanks!!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale
to see if it is there?
Also look at the aparc+aseg.mgz to see how big the cortical region for
caudalanteriorcingulate is. The wmparc is based on the aparc part of aparc+aseg.
doug
On 8/5/13 12:49 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
I'm looking at stats/wmparc.stats
-5454
On 8/6/13 9:33 AM, Bruce Fischl
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
yes, if they are surface-based then it is really trivial (just give them to
mris_anatomical_stats with the -l label name flag)
cheers
Bruce
On Tue, 6 Aug 2013, Yang, Daniel wrote:
Dear
, create and save the labels
you want, then run mri_segstats using the label and thickness as input.
doug
On 08/06/2013 10:00 AM, Yang, Daniel wrote:
Hi Bruce,
Thanks for your reply. Those functional ROIs are volume-based (that
is, generated by spm/fsl/BrainVoyager).
So it seems that I need
...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
On 08/06/2013 02:49 PM, Yang, Daniel wrote:
Thanks, Doug, for the procedure. I'm just wondering how the ROI
sampling is performed.
May I ask three questions?
(a) when you say sample the ROIs from the fMRI space to the surface,
are you referring to white
Dear FS Experts,
My model has two categorical variable: Diagnosis and Sex. I am interested in
the effect of Diagnosis but I want to control the Sex effect. Toward this goal,
I want to model two main effects and want to avoid modeling their interaction
term. Is this something feasible in
) 737-5454
On 9/3/13 8:45 PM, Yang, Daniel
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:
Dear FS Experts,
My model has two categorical variable: Diagnosis and Sex. I am interested in
the effect of Diagnosis but I want to control the Sex effect. Toward this goal,
I want to model two
(203) 737-5454
On 9/4/13 10:10 PM, Douglas Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
I'm not sure you can do that with a linear model. What would your model look
like?
doug
On 9/4/13 9:18 PM, Yang, Daniel wrote:
Hi Freesurfer,
Is it possible to specify only two
...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
what does a slope of Sex mean? Is Sex a continuous variable?
On 09/05/2013 11:03 AM, Yang, Daniel wrote:
Hi Doug,
So I have two variables: Diagnosis (patient vs. control) and Sex
(female vs. male).
My model would be:
cortical thickness
seen it
done before and don't recommend it, but if you want to do it, set up a
FSGD file with one group (eg, Main) and two variables. See the FSGD page
on the wiki
doug
On 09/05/2013 03:04 PM, Yang, Daniel wrote:
Sex is a nominal variable but can be coded as 0,1.
If it's coded as 0 (male), 1
Hi Freesurfer experts,
Does qdec_glmfit support the option of specifying nuisance factors?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
___
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Hi FreeSurfer experts,
Let's say I have two class variables:
Sex (female, male)
Dx (patient, control)
I see that the analysis results show the following:
Does the average thickness, accounting for Dx, diff between female and male?
Red means: female male
Does the average thickness,
Hi FreeSurfer Experts,
On this page
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons),
it says: In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding
to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common
thresholds.
I am
-value. It is -log10(p), so -log10(.01) = 2
doug
On 9/7/13 9:13 PM, Yang, Daniel wrote:
Hi FreeSurfer Experts,
On this page
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons),
it says: In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding
to p-values
, there is no difference. Once you select the appropriate threshold,
it does not matter whether it is a z-field, p-field, t-field, or
-log10(p)-field because it gets binarized.
doug
On 9/8/13 9:33 PM, Yang, Daniel wrote:
Hi Doug,
Thanks! I didn't realize that the threshold is a negative exponent to a base of
10
Dear all,
Is there a way to convert .mgh to .label? My .mgh is a ROI file from qdec-based
group analysis and I don't want to draw the ROIs manually.
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
mri_annotation2label. Otherwise use Gari's suggestion.
doug
On 09/09/2013 03:00 PM, Garikoitz Lerma-Usabiaga wrote:
Hi Daniel,
you can use mri_surfcluster.
br,
Gari
On Mon, Sep 9, 2013 at 8:25 PM, Yang, Daniel yung-jui.y...@yale.edu
mailto:yung-jui.y...@yale.edu wrote:
Dear all
(203) 737-5454
On 9/9/13 6:40 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
You cannot. You will have to do the conjunction on the cluster sig
files, then extract a label from that.
On 09/09/2013 06:30 PM, Yang, Daniel wrote:
Thanks so much! I used
Hi all,
The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if
they are based on the Talairach system or some sort of MNI-Talairach system. If
the latter, can you tell me something more about it? Like a webpage that
describes its relationship between the MNI152 or the
Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
It is an estimate of Tal coords from the MNI305. See
http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
If you want MNI305, run mri_surfcluster with --nofixmni
doug
On 09/10/2013 05:08 PM, Yang, Daniel wrote:
Hi all
Hi all,
I know I can use mri_label2label and then mris_anatomical_stats -l to obtain
the label-based cortical thickness for each individual subject.
I also know that there is a tool called mri_annotation2label.
But is there a way to convert annotation to each individual subject, so that I
can
? It will probably be
hard to tell since the matrix is pretty close to identity.
doug
On 09/10/2013 05:17 PM, Yang, Daniel wrote:
Thanks, Doug. I am really hoping to get MNI152 (because I also use
fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?
Best,
Daniel
--
Yung-Jui Daniel
Just my two cents:
I think the age should be mean-centered; otherwise, the meaning of the other
variables need to be interpreted as age = 0 (rather than mean age = 0).
In general, I believe in qdec or mri_glmfit, the effects of Class variable are
interpreted as 0 on the continuous/nuisance
you can refer to this post:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31297.html
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 9/12/13 9:04 AM, Anita van Loenhoud
without going through the talairach itself.
When FS computes Tal coords, it does so nonlinearly.
doug
On 9/11/13 12:08 PM, Yang, Daniel wrote:
Hi Doug,
It's pretty awesome. So accordingly,
MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) *
1
MNI152y = (0.0146) MNI305x
Hi all,
I performed cluster analyses and obtained several clusters, which are indicated
by the corresponding maximum significance levels. For example, cluster one --
4.00, and cluster two -- 4.00.
Then I did a conjunction analysis to see their overlap, and then did a
mri_surfcluster to get
nonlinearly.
doug
On 9/11/13 12:08 PM, Yang, Daniel wrote:
Hi Doug,
It's pretty awesome. So accordingly,
MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) *
1
MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1
MNI152z = (-0.0130) MNI305
Dear FreeSurfer Experts,
If I have a label that spans across multiple anatomical regions, is it possible
to automatically break it down according to aparc.annot?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
to functional threshold and up to
different labels check (not sure of the exact wording).
6. Left click in a region that you want, and click fill.
7. Save the label.
8. Right click to unselect and go to 6 until you are done with all the
subregions
cheers
Bruce
On Sun, 22 Sep 2013, Yang, Daniel
Hi FreeSurfer Experts,
Is it possible to dilate a label using command line?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
___
Freesurfer mailing list
will do this, at least the current dev version and
maybe 5.3:
mri_label2label | grep dilate
--dilate Ndilate the label N times before writing
cheers
Bruce
On Mon, 23 Sep 2013, Yang, Daniel wrote:
Hi FreeSurfer Experts,
Is it possible to dilate a label using command line?
Thanks!
Daniel
It seems that only in dev version, mri_label2label supports dilation.
But I find that in 5.3, mris_label_calc is able to perform dilation too!
Best,
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 9/22/13 9:38 PM, Yang, Daniel
New Haven, CT
(203) 737-5454
On 9/23/13 3:40 PM, Yang, Daniel
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:
Dear FreeSurfer Experts,
Is there a way to use command line to obtain the stats (e.g., area) for a given
label?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral
Dear FreeSurfer Experts,
Is there a way to use command line to obtain the stats (e.g., area) for a given
label?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
___
Freesurfer
wrote:
Hi Daniel
you can give it to mris_anatomical_stats with the -l label command
cheers
Bruce
On Mon,
23 Sep 2013, Yang, Daniel wrote:
Dear FreeSurfer Experts,
Is there a way to use command line to obtain the stats (e.g., area) for a given
label?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Dear FreeSurfer Experts,
I am trying to visualize fMRI activation (generated from fsl) on the fsaverage
inflated surface, using mni152.register.dat.
It's odd that I find the results to be slightly different between tksurfer and
freeview. However, I made sure that I am using the same
On 9/26/13 12:26 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
They might be sampling to different surfaces. To make sure they show the
same exact thing, try mapping the data to the surface with mri_vol2surf
doug
On 09/25/2013 08:31 AM, Yang, Daniel wrote
some sort of inverse mni152.register.dat
somewhere?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 9/27/13 6:44 AM, Yang, Daniel
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:
Thanks Doug!
Because it maps
N Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
The way the software is set up, you should use mni152.register.dat with
mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces
doug
On 10/01/2013 05:49 PM, Yang, Daniel wrote:
Hi Doug,
Just checking
Dear FreeSurfer Experts,
Is there a program that can automatically judge whether a mgh is in the rh or
lh?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
___
Freesurfer mailing
.
On 10/01/2013 07:45 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
Is there a program that can automatically judge whether a mgh is in
the rh or lh?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
Dear FreeSurfer Experts,
Is there a way to estimate the SNR in MPRAGE scans besides using wm-anat-snr ?
For examples, I read that SNR is improved in multiecho MPRAGE and I am
wondering how that is computed?
Thanks!
Daniel
___
Freesurfer mailing list
Dear FreeSurfer creators and experts,
I am trying to run qdec with one discrete with three levels (i.e.,
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error
message:
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y …
I am wondering if
for more details.
doug
On 2/16/14 4:53 PM, Yang, Daniel wrote:
Dear FreeSurfer creators and experts,
I am trying to run qdec with one discrete with three levels (i.e.,
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error
message:
ERROR: no contrasts specified.
Error
Dear FreeSurfer developers and experts,
If I have a binary factor (Group1: patients, Group2: controls) and a continuous
variable (age), I know I can follow Contrast2 in the following wiki to test the
interaction effect.
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V
Contrast2: [0 0 1
Dear FreeSurfer experts,
I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV),
and 1 nuisance factor (NUI). I want to make sense of some specification of the
regressors and contrasts.
Because they are not described in
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I
doug
On 02/18/2014 10:08 AM, Yang, Daniel wrote:
Dear FreeSurfer experts,
I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate
(COV), and 1 nuisance factor (NUI). I want to make sense of some
specification of the regressors and contrasts.
Because they are not described
in http
: yung-jui.y...@yale.edu
On 2/18/14 2:13 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
It will tend to weight smaller groups by a proportion greater than the
number of subjects in the group.
On 02/18/2014 01:58 PM, Yang, Daniel wrote:
Thanks Doug! One
Dear FreeSurfer Experts,
In this webpage (http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples), it
says Two Groups (1 Factor, Two Levels), Two Covariates. DODS only. QDEC-able.
However, I cannot select more than one covariate in qdec. Any suggestion? I'm
using qdec in Mac, FreeSurfer 5.3.
Sorry, I've found an answer to this here:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32928.html
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
On 2/19/14 6:47 PM, Yang
...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
Let's say you have four groups with 10 20 30 40 (100 total). The first group
would get a weight of .25 where it only had 10% of the total. I don't think
there is any way around this.
On 2/18/14 4:07 PM, Yang, Daniel wrote:
Doug, sorry, I am
Dear FreeSurfers,
I have two discrete and binary factors (Dx: patients vs. controls; Sex: female
vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is
a 3-way interaction of Dx x Sex x Age, regressing out IQ, is the following
interpretation correct?
Red/yellow: In
Dear FreeSurfer Experts,
In the example here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V, it
describes the testing of the main effects of two continuous variables.
In order to test the interaction effect, I think we can form an interaction
term like age x weight as the third covariate,
to come up with a sentence like the one you
are trying to state
doug
On 02/20/2014 02:25 PM, Yang, Daniel wrote:
Dear FreeSurfers,
I have two discrete and binary factors (Dx: patients vs. controls;
Sex: female vs. male), one continuous variable (Age), one nuisance
factor (IQ). If there is a 3-way
Dear FreeSurfers,
I obtained a file from cluster analysis, called cache.th20.pos.sig.ocn.mgh
Can you tell me what OCN stand for? And what is this file for? I tried to view
it but was unable to see anything.
Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study
Dear FreeSurfer experts,
Is it possible to display two labels in tksurfer or freeview, where one label
is outlined with a certain color and the other label is filled with a different
color?
I want to show two labels, one is within the other one.
If yes, could you please tell me the specific
labels and create an annotation with mris_label2annot (you
get to specify the color)
doug
On 02/26/2014 05:12 PM, Yang, Daniel wrote:
Dear FreeSurfer experts,
Is it possible to display two labels in tksurfer or freeview, where
one label is outlined with a certain color and the other label is
filled
this. For the other
stuff, look at the help for mris_label2annot --help
doug
On 02/26/2014 05:35 PM, Yang, Daniel wrote:
Doug,
Thanks for your reply! In the annotation, can one of the label be just
outlined and the other filled?
I would really appreciate if you could provide a step-by-step example
to do it. You don't even need to save it as an mgz. You
can just do tools-labels-copy label stats to overlay, then delete the
label and you have an overlay from it (assuming the label-stat field is
not zero)
On Thu, 27 Feb 2014, Yang, Daniel wrote:
Thanks for both of you for the helps! I also find
...@nmr.mgh.harvard.edu wrote:
that's a good way to do it. You don't even need to save it as an mgz. You
can just do tools-labels-copy label stats to overlay, then delete the
label and you have an overlay from it (assuming the label-stat field is
not zero)
On Thu, 27 Feb 2014, Yang, Daniel wrote:
Thanks for both of you
...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
mri_morphology for the .mgz
for the label you can do it in tksurfer in the tools-label menu or use
mri_label2label (at least I put it in the dev version, not sure if it is
released yet)
On Thu, 27 Feb 2014, Yang, Daniel wrote:
By the way, what command
Dear FreeSurfer Experts,
FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can
have WM vol as the DV in these tools with the same GLM model? For example, I
want to test the WM regions that is most strongly positively correlated with a
given factor.
Thanks!
Daniel
:18 PM, Yang, Daniel
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:
Dear FreeSurfer Experts,
FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can
have WM vol as the DV in these tools with the same GLM model? For example, I
want to test the WM regions
Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
On 3/2/14 7:18 PM, Yang, Daniel
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:
Dear FreeSurfer Experts,
FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can
have
12:58 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
you can just add them into your qdec file (from wmparc.stats)
doug
On 03/02/2014 07:18 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
FS provides thickness as the DV in qdec and mri-glmfit. Do you know
wmparc.stats (not wmparc_stats.txt)
On 03/03/2014 01:07 PM, Yang, Daniel wrote:
Thanks, Doug! But that is about using wmparc.stats as IV or
continuous/covariate variables. I would like to use WM vol as the DV
(measure).
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New
wrote:
It should be there if the recon did not fail. The file is called
wmparc.stats (not wmparc_stats.txt)
On 03/03/2014 01:07 PM, Yang, Daniel wrote:
Thanks, Doug! But that is about using wmparc.stats as IV or
continuous/covariate variables. I would like to use WM
, Yang, Daniel wrote:
Sorry, I wasn't clear. It's a cortical label that I manually created,
based on the pial surface.
Is it possible to generate the corresponding WM vol based on a new
label (not pre-defined)?
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New
Dear FreeSurfer Experts,
I would like to extract the mean thickness for each subject, and I can see that
in the lh.aparc.stats, there are three lines. For example:
# Measure Cortex, NumVert, Number of Vertices, 107414, unitless
# Measure Cortex, WhiteSurfArea, White Surface Total Area, 73280.4,
automatically includes these measures. Can you check?
And, yes, mean thickness can be computed as (lh+rh)/2
doug
On 3/30/14 12:58 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
I would like to extract the mean thickness for each subject, and I can see that
in the lh.aparc.stats, there are three
Dear FreeSurfer group,
If I want to extract frontal WM volume, is it something doable in FreeSurfer?
Much obliged,
Daniel
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The
and add up the volumes. If you have another way to define
frontal, then you'd have to tell us what that is.
doug
On 05/14/2014 05:37 PM, Yang, Daniel wrote:
Dear FreeSurfer group,
If I want to extract frontal WM volume, is it something doable in FreeSurfer?
Much obliged,
Daniel
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using
mri_annotation2label, I am running if it is possible to obtain NIfTI files
associated with aseg parts?
Thanks!
Daniel
___
Freesurfer mailing list
, 2014, at 5:54 PM, Yang, Daniel yung-jui.y...@yale.edu
wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation
using mri_annotation2label, I am running if it is possible to obtain
NIfTI files associated with aseg parts?
Thanks!
Daniel
neighbor
Cheers
Bruce
On Jun 15, 2014, at 10:28 PM, Yang, Daniel yung-jui.y...@yale.edu
wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very
flexible. I meant to obtain the aseg individual label files in MNI152
space as NIfTI files, for example, the different
Dear all,
While there is the file
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat, there is no
such file as:
${FREESURFER_HOME}/subjects/fsaverage/mri/reg.1mm.mni152.dat or
${FREESURFER_HOME}/subjects/fsaverage/mri/transforms/reg.1mm.mni152.dat ?
I am wondering how we can
.1mm.mni152.dat? Or how can I
generate one?
Thanks!
On 6/16/14, 3:51 AM, Douglas Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:
Sorry, what are you trying to do with that vol2vol command? The command
line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote
was trying to find out what it is you are trying to do, not what your
command line is. The command may run, it is not doing anything intelligible,
ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm
mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel
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