eesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:
>it's usually a bit less than that - aroudn 140K or so
>Bruce
>
>On Mon, 29 Feb 2016,
>Yang, Daniel wrote:
>
>> Hi Bruce,
>>
>> Is it okay to say that it is approximately 160,000 vertice
Dear FreeSurfer experts,
Can you please indicate the number of vertices FreeSurfer use in each
hemisphere to reconstruct the brain (e.g., cortical thickness)? Is there a
fixed number or an approx. number?
Many thanks,
Daniel
--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail:
gt;of the white matter for each hemisphere.
>
>cheers
>Bruce
>
>
>On Mon, 29 Feb 2016, Yang, Daniel wrote:
>
>> Dear FreeSurfer experts,
>>
>> Can you please indicate the number of vertices FreeSurfer use in each
>>hemisphere to reconstruct the brain
Just to note for people who are interested:
It does seem that when voxel-to-ras determinant > 0, then the file is
neurological.
--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
On 1/26/16, 10:09 PM, "Yang, Daniel" <daniel.yj.y...@yale.edu>
ecessarily. For FSL, the determinant must be less than 0 (see
>mri_info output). Having said that, even if the det<0, it may still show
>up funny in fslview
>
>On 01/25/2016 12:11 PM, Yang, Daniel wrote:
>> Dear FreeSurfer experts,
>>
>> I find that mri_convert will
eesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:
>If the determinant is less than 0, then it is radiological (probably it
>will be radiological).
>
>On 01/26/2016 04:20 PM, Y
Dear FreeSurfer experts,
I find that mri_convert will convert DICOM of structural scan to neurological
orientation by default.
For example, mri_convert --in_type dicom --out_type mii
Thus, the NII may need to be swapped in x for use in FSL.
In this the case?
Many thanks,
Daniel
--
Daniel
gh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TalX TalY TalZ
If you use --fixmni, then they are reported in approximate talairach space
On 11/11/15 10:08 AM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
Are these coordinates reported in mri_surfcluster
Dear FreeSurfer Experts,
Are these coordinates reported in mri_surfcluster in MNI305 space? (with
—fixmni)
Thanks,
Daniel
--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:
>There should be a t.mgh file there (or maybe F.mgh). You can just pull
>the value out of the vertex out of that.
>
>On 11/9/15 6:46 PM, Yang, Daniel wrote:
>> Hi Doug,
>>
Dear FreeSurfer Experts,
Is it possible to convert a label file to a surface-based mgh file? Could you
please provide an example (e.g., on a white surface)?
Best,
Daniel
--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
___
Dear FreeSurfer experts,
In the output mri_surfcluster (e.g.,
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary),
what is the statistics behind the Max?
Is it either t-statistic (if only 1 line of contrast) or F-statistic (if two
lines of contrast), but not
eesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:
>use mri_label2label with the --mask option
>
>On 11/09/2015 01:34 PM, Yang, Daniel wrote:
>> Dear FreeSurfer Experts,
>>
>> Is it possible to convert a label file to a surface-based mgh file?
rd.edu> wrote:
>
>
>On 11/09/2015 10:51 AM, Yang, Daniel wrote:
>> Dear FreeSurfer experts,
>>
>> In the output mri_surfcluster (e.g.,
>>
>>https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisCluster
>>Summary),
>> what is the statis
> wrote:
>Hi Daniel,
>
>you can always specify your own design matrix X in mri_glmfit. So just
>create those columns, fit and test. Of course you need to make sure that
>the order of subjects in Y is identical with the one used in X.
>
>Cheers, Martin
>
>On 11/06
Dear FreeSurfer experts,
I have a group variable (X) with two levels and I want to test if there is a
curvilinear interaction with age (Z). Can this be tested in FreeSurfer?
Specifically, the model would be
Y = b0 + b1X + b2Z + b3Z*Z + b4X*Z + b5X*Z*Z + error
I want to test b5 while
Dear FreeSurfer Experts,
When I perform aparcstats2table —meas area, does it get it pial.area or white
area?
I believe it is the pial.area, but this is not documented. If yes, what can I
obtain white area via aparcstats2table?
Thanks,
Daniel
--
Daniel Yang, Ph.D.
Yale Child Study Center
Hi all,
Found an answer here:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036542.html
It works for me!
Best,
Daniel
From:
>
on behalf of Daniel Yang
Dear FreeSurfer Experts,
When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option.
Could you please advise how I can obtain an individual’s pial_lgi value, give a
label?
Many thanks!
Daniel
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Dear FreeSurfer experts,
I have a number of *.cluster.mgh files and I would like to calculate their
difference and peak coordinate etc like in fslmaths or fslstats in FSL.
For example, given two images, I want to know the brain regions in image1 but
not in image2.
Could you please recommend
n always convert to nifti via:
>
>mri_convert cluster.mgh cluster.nii
>
>and you will be able to use the FSL tools
>
>cheers
>Bruce
>
>
>On Tue, 3 Nov 2015, Yang, Daniel
>wrote:
>
>> Dear FreeSurfer experts,
>>
>> I have a number of *.cluster.mg
cheers
Bruce
On Thu, 6 Aug 2015, Yang, Daniel wrote:
Hi Bruce,
Thanks so much! From the output of mris_anatomical_stats, I can see that
it affects the following three variables:
GrayVol ThickAvg ThickStd
When sulc is used instead of thickness, do you know what the meaning of
these three
Dear FreeSurfer Experts,
Is there a way to obtain sulcal depth in a given region (label) for a
particular subject?
Many thanks!
Daniel
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Freesurfer@nmr.mgh.harvard.edu
2015, Yang,
Daniel wrote:
Dear FreeSurfer Experts,
Is there a way to obtain sulcal depth in a given region (label) for a
particular subject?
Many thanks!
Daniel
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https
. For subcortical structures you are better off showing the
results in slices.
cheers
Bruce
On Mon, 23 Feb 2015, Yang, Daniel wrote:
Hi Bruce,
Thanks for the reply. My main question is how to best visualize subcortical
activation in a figure.
Sometimes we do see some subcortical activation (like
a surface for, but I'm still not sure what you
are trying to do.
cheers
Bruce
On Fri, 20 Feb 2015, Yang, Daniel wrote:
Hi Bruce,
Thanks! and yes, I used mri_vol2surf to convert subcortical region as a
volume file to surface (mgh file) and then visualize it with tksurfer.
According to what you
Dear FreeSurfer experts,
The following command works but how do I get the labels from —a2009s ?
mri_annotation2label --a2005s --subject fsaverage --hemi rh --outdir .
What is the difference between a2005s and a2009s?
Thanks!
Daniel
___
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@nmr.mgh.harvard.edu
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] extract individual label from Destrieux Atlas
Use --annotation a2009s.aparc
On 2/19/15 8:34 PM, Yang, Daniel wrote:
Dear FreeSurfer experts,
The following command works but how do I get
Dear FreeSurfer experts,
I find that tksurfer allows me to visualize subcortical areas such as
hippocampus. The visualization looks valid to me.
Can tksurfer be used in this way?
Thanks!!
Daniel
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Daniel
no, tksurfer visualizes surfaces exclusively, and the subcortical
structures are volumetric by and large. You could tesselate their surface
and view it in tksurfer, or just use tkmediit or freeview.
cheers
Bruce
On Thu, 19 Feb
2015, Yang, Daniel wrote:
Dear FreeSurfer experts,
I find
Dear all,
I found that mri_label2label generates different results, depending on whether
the software’s platform is MacOS Lion or CentOS 6.
Is this possible?
Thanks!
Daniel
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Bruce
On Thu, 19 Jun 2014, Yang, Daniel wrote:
Dear all,
I found that mri_label2label generates different results, depending on
whether the software¹s platform is MacOS Lion or CentOS 6.
Is this possible?
Thanks!
Daniel
___
Freesurfer
? Is the difference between 1 and 3 trivial?
Thanks!
Daniel
On 6/19/14, 8:13 PM, Yang, Daniel
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:
Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.
Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?
Thanks,
Daniel
On 6/19
it was a bug we fixed after the release. We can send you new
versions on those operating systems and you can try them out.
Zeke: can you get Daniel new versions of mri_label2label?
thanks
Bruce
On Fri, 20 Jun 2014, Yang,
Daniel wrote:
Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.
Do you mean
On Jun 19, 2014, at 10:20 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
Yes, it was only mri_label2label has that bug
On Jun 19, 2014, at 10:14 PM, Yang, Daniel
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:
Thanks! Is there a list of bug fixed
use the one from mri/
The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to
do the opposite. You can see that the right_amygdala.mgz I have as the input
On 6/17/14 1:10 PM, Yang, Daniel wrote:
Hi Doug,
Could you show us the full command of performing such a registration? Very
curious! Thanks.
Best,
Daniel
From: Douglas Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list
freesurfer
segment NIFTI files
They look pretty similar. I doubt that there will be much practical difference.
On 6/17/14 3:08 PM, Yang, Daniel wrote:
Hi Doug,
Thanks! I ran this: bbregister --mov
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg
1mmreg.dat --init-fsl
And obtained
.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
registration. Use
$FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat
specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec
--interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files
files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/
The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to
do the opposite. You can see
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
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, 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
Dear FreeSurfer group,
If I want to extract frontal WM volume, is it something doable in FreeSurfer?
Much obliged,
Daniel
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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 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
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,
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
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,
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 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 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 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 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,
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
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.
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
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
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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
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
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,
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
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
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
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
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
(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
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