Hello list,
I have a question regarding what stats are more correct to use to get
whole hemisphere surface area and mean thickness.
The cortex.label values extracted using the two bottom command lines
don't match aparc stats, however they match in the number of vertices
between them, and us
Ciao Lilla,
Thank you so much for the quick answer. Sorry to bother you again but I've
got some other questions to ask.
First of all how have you managed to obtain reasonable recons with patients
of 3-4 years old? There is a pipeline or particular settings to follow and
if yes which ones? Then I w
Dear FreeSurfer experts,
Hello everyone. I am a beginner of Freesurfer. And I want to do
parcellation using some templates (are there any accurate templates in surface
space?) in the inflate brain after “recon -all” . After that I wish to get some
individual areas like M1,SMA and so on i
Hi Freesurfer experts,
I have a volume label only which is only different from zero in the
white matter-gray matter boundary. I am trying to convert this volume
label to a surface label in order to visualize it in tksurfer. I am
using mri_vol2surf:
mri_vol2surf --mov volume_label.nii --out vol
Hi Karen
This is typically caused because the surface just misses the voxels that
have your label in some points. You can either thicken the label in the
volume, or use morphological operations like close (in mri_label2label or
manually in tksurfer) to fill the holes
cheers
Bruce
On Mon, 2
Hi Bruce,
Thanks for your answer. I will like to do it automatically as I have a
lot of labels. However, I can't find an option called close in
mri_label2label. Can you give me another hint?
Best,
Karen
On 03/24/2014 03:24 PM, Bruce Fischl wrote:
Hi Karen
This is typically caused because
Yes, that is the plan. Currently we are only using T1 data, but might also
consider multiple channels.
Lilla
On Mon, 24 Mar 2014, Alexopoulos, Dimitrios wrote:
will this future pipeline include processing neonatal data? If so, will it use
both T1/T2 acquisitions?
Thanks. JIm
__
Try using the --paint option to mri_label2label
doug
On 3/24/14 10:53 AM, Karen Marie Sandø Ambrosen wrote:
Hi Bruce,
Thanks for your answer. I will like to do it automatically as I have a
lot of labels. However, I can't find an option called close in
mri_label2label. Can you give me anoth
In theory, it should be possible. I have not used Jorge's stream, so I
don't know that much about it. Does it save an estimate of the FWHM? If
so, then you can run mri_surfcluster passing it the p-value (ie,
-log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. This is
what mri_glmfi
In that case, you can just do a paired analysis. Do a search for that on
the wiki and you'll find examples
doug
On 3/21/14 5:50 PM, Peggy Skelly wrote:
The actual time between tp1 & tp2 varies for subjects, *but* every
subject received the same "dose" of treatment between timepoints. To
ask
On 3/23/14 6:46 AM, Eileen Moore wrote:
> Hello FreeSurfer experts,
>
> I am using freesurfer v5.3 on a linux os. I have a few questions regarding
> individual aseg statistics (volume, intensity) for a subcortical region that
> is not automatically segmented by freesurfer. Using tkmedit I have m
On 3/23/14 2:47 PM, Tudor Popescu wrote:
Hi Doug,
> 3) In a group X gender X age DODS design, exactly which contrast
> (interaction) has to be examined in order to see if the analysis
> proceeds as DODS or as DOSS? And what would the course of action be
> assuming there are sign
How much of a difference is there? There should not be much, but there
will be some because the aparc does not cover the exact same vertices as
cortex.label
doug
On 3/24/14 8:04 AM, _andre...@sapo.pt wrote:
> Hello list,
>
> I have a question regarding what stats are more correct to use to ge
Hi
I would like to analyse local gyrification data for a number of brains in
Matlab. I have ran the command
mris_compute_lgi -i lh.pial
which results in a file called lh.pial_lgi. However, I was expecting an output
of the form lh.pial_lgi.mat which could be immediately read into Matlab. Do you
Hi Karen
you need to grab a new version then:
mri_label2label --help|grep close
--close N close the label N times before writing
--paint dmax surfname : map to closest vertex on source surfname if d
< dmax
the closest surface vertices:
what hardware/software environment are you r
Hi,
B1 field correction was collected during the scan. My question is how it can
be used in the surface reconstruction?
Thanks,
Xiaomin Yue ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr
Hi Xiaomin
can you be more specific? What kind of B1 field map did you collect? Do
you mean B1 transmit or receive?
cheers
Bruce
On Mon, 24 Mar 2014, Xiaomin Yue wrote:
Hi,
B1 field correction was collected during the scan. My question is how it can
be used in the surface reconstruction?
Is this the difference you mean?
[t:D:mri-> grep Cortex ~/tmp/lh.total.stats
# Measure Cortex, NumVert, Number of Vertices, 118847, unitless
# Measure Cortex, SurfArea, Surface Area, 78090, mm^2
[t:D:mri-> grep Cortex ~/tmp/lh.aparc.stats
# Measure Cortex, NumVert, Number of Vertices, 111237, un
Dear Kim,
This may be of interest to you:
http://dx.plos.org/10.1371/journal.pone.0038234
Cheers,
Ed
On 24 Mar, 2014, at 17:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 3
Date: Mon, 24 Mar 2014 12:28:29 +0900
From: jh kim
Subject: Re: [Freesurfer] Difference in volumes btw 5.
I was also referring to the surface area and thickness (looking at the
files originated from white matter, which is also the default for
aparc I think):
For surface area
aparc= 72998.7
total= 72999
cortex=78090
For CT
aparc= 2.422
total= 2.422
cortex= 2.313
And also, which volume measure
Sorry, what is the difference between total and aparc?
On 03/24/2014 01:29 PM, _andre...@sapo.pt wrote:
> I was also referring to the surface area and thickness (looking at the
> files originated from white matter, which is also the default for
> aparc I think):
>
> For surface area
> aparc= 7299
Dear all,
I would like to capture regions where the gray matter/ white matter
junction is blurred in order to detect possible focal cortical dysplasias.
As I understood the WM/GM segmentation is done by the script mri_segment.
Would it be possible detect those regions where the gradient between
Hi Markus
I would think that looking at the gray/white contrast across the ?h.white
surface would be more informative
cheers
Bruce
On Mon, 24 Mar 2014, Markus Gschwind
wrote:
Dear all,
I would like to capture regions where the gray matter/ white matter junction is
blurred in order to dete
Hi Doug,
I recently saw your solution to a reported problem with grabbing StrictLobes WM
& GM (posted on the Freesurfer forum 12/04/2013; thread title= major lobes).
I have successfully grabbed the StrictLobes WM, but I am having trouble with
the GM.
According to the forum (posted 12/04/2013),
what version of FS do you have and what is your platform?
doug
On 03/24/2014 02:34 PM, Juranek, Jenifer wrote:
>
> Hi Doug,
>
> I recently saw your solution to a reported problem with grabbing StrictLobes
> WM & GM (posted on the Freesurfer forum 12/04/2013; thread title= major
> lobes).
> I hav
Hi Markus
I wouldn't use brainmask as it has been normalized too aggressivley. Maybe
the nu.mgz. Look at the difference between values just outside of it and
just inside of it
cheers
Bruce
On Mon, 24 Mar 2014, Markus Gschwind wrote:
Dear Bruce,
Thanks for the rapid answer!
Do you mean th
Dear Bruce,
Thanks for the rapid answer!
Do you mean that I take the voxel values of brainmask.mgz at the place
where the ?h.white surface passes, right?
I thought that the ?l.white surface marks the limit between GM and WM as a
result of a binary decision.
I would be interested in the local cer
Hi list,
I'm performing TRACULA on three groups for all 18 tracts and for FA, MD, RD, AD.
Which is the best way to perform statistic on TRACULA outcomes? I think that
MANCOVA is too hard and it delete interesting and consolidate (in literature)
results.
Thanks,
Stefano __
Ciao Stefano,
can you be a bit more specific about what you're exactly trying to to?
Am I correctly assuming that you are looking at differences between your
groups? Are you looking at average FA/MD/RD/AD over whole tracts, or at
values along them? Do you have any strong hypothesis on which tract w
CentOs 6 running FS v 5.1.0. on the workstation where we have processed about
300 datasets.
Many Thanks!
Jenifer
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 24, 2014 2:44 PM
To: Juranek, Jenifer
Cc: freesurfer@nmr.mgh.harvard.edu
Subje
Ciao Eugenio,
thank you very much for your prompt and kind response.Yes, I'm looking average
over the entire support of the path distribution and their differences among 2
pathological and 1 control groups.I haven't a strong hypothesis.When I
performed MANOVA, Tukey or Bonferroni post hoc find d
Hi again,
if you perform the same analysis over and over for each of the 18
tracts, then the Bonferroni corrected p-value would be 0.05/18
Cheers,
/Eugenio
On Mon, 2014-03-24 at 22:47 +0100, std...@virgilio.it wrote:
> Ciao Eugenio,
>
>
> thank you very much for your prompt and kind response.
>
Unless you're comparing groups in a pairwise manner, i.e., A vs B, B vs
C, and A vs C. In that case, you would have 18 x 3 comparisons and the
threshold for significance would be 0.05 / (18 x 3)
Cheers,
/Eugenio
On Mon, 2014-03-24 at 17:50 -0400, Juan Eugenio Iglesias wrote:
> Hi again,
> if you p
Hi Bruce!
Ok I see, great! Tank you!
So to double check, this will be something like :
mri_vol2surf \
--mov /mri/nu.mgz \
--ref /mri/nu.mgz \
--surf /surf/lh.white
--projdist mmdist -2 \ # for inside white
# --projdist mmdist 2 \ # for outside white
--interp trilinear \
--hemi
it really depends on the size of the abnormality. I would guess 2 is too
big, and you want something more like 1, and sampling not averaging
On Mon,
24 Mar 2014, Markus Gschwind wrote:
Hi Bruce!
Ok I see, great! Tank you!
So to double check, this will be something like :
mri_vol2surf \
-
you might want to look at the pctsurfcon script to see if that gets you
where you want to be
On 03/24/2014 06:18 PM, Bruce Fischl wrote:
> it really depends on the size of the abnormality. I would guess 2 is
> too big, and you want something more like 1, and sampling not averaging
> On Mon, 24
Hi,
I have posted a question about the error while using recon-all command with
-use–gpu option on a CentOS 6 machine a while back.
CUDA Error in file 'mriconvolve_cuda.cu' on line 945 : unload of CUDA runtime fa
iled.
Abort (core dumped)
ERROR: mri_ca_register with non-zero status 134
The probl
Whow that is great!! Thank you so much Doug, I was not aware of this!
That's what I needed it seems.
Thanks Bruce and Doug!
Markus
2014-03-24 23:21 GMT+01:00 Douglas N Greve :
>
> you might want to look at the pctsurfcon script to see if that gets you
> where you want to be
>
> On 03/24/2014 06:
Hi Doug,
Is 'pctsurfcon' intended to supersede 'mri_cnr'? If not, what are the
intended situations in which one would be used over the other?
thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Wa
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