Dear Doug
this is a snapshot of the website
(https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) where the
categorical variable "group" is coded as a number (see point 4)
**
Example data an
Dear FS team,we are using Philips Achieva 3T scanner for acquiring our MRI data.Our T1-weighted MRI protocol as follows:- 3D T1 TFE coronal- 0.5x0.5x1.0 voxel resolution- FOV 240x240 mm- TR/TE = 9.8/4.6 ms- Spacing between slices: 0.5 mm- NSA (=NEX=ACQ) = 1- Bandwidth = 142 Hz/PxIn our most
Hi Prasser:
Did you set the environment for MATLAB e.g.,
setenv MATLABPATH /Applications/MATLAB_versionsetenv PATH
${MATLABPATH}/bin:${PATH}
This is required for FS to source MATLAB.
best,
Alan
On Thu, Sep 29, 2016 at 6:46 PM, prasser wrote:
> Hi, Reposting. Thanks.
>
> On Tue, 27 Sep
Hello,
I am trying to take nay volume that is registered and create an inflated
surface. I am trying to use mri_vol2surf. I am having problems with the
registration source. From the examples I could fine, it should be --srcreg
*.dat. The only *.dat file I have is segment.dat which does not work
Hi Gajendra,
The recon stream exists in a beta version and will not make it to 6.0. I
am hoping to release the stream and the atlas though before the end of the
year.
Lilla
On Thu, 29 Sep 2016, GAJENDRA KATUWAL (RIT Student) wrote:
Hello FreeSurfer experts,
I am considering using Freesur
Thank you so much for the reply Lilla.
Lilla and Freesurfer community,
I have few more questions.
Before the Freesurfer compliant default pediatric atlas is not released, my
option would be to use age specific pediatric atlases from other sources
such as:
1. Sanchez et al. pediatric atlases
You have to run recon-all to get the surfaces of a volume.
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna wrote:
> Hello,
>
> I am trying to take nay volume that is registered and create an inflated
>
I already ran recall-all. I am trying to create a different surface not created
using recon-all.
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
[trisanna.sprung-m...@mail.mcgill.ca]
Se
Hi Anna
I think you are trying to project an overlay on a surface, not create a
surface, right?
Bruce
> On Sep 30, 2016, at 10:44 AM, Crawford, Anna wrote:
>
> I already ran recall-all. I am trying to create a different surface not
> created using recon-all.
>
> Anna
> From: freesurfer-boun..
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know
this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays
No problem. I'm not exactly sure, but I think I just want a surface overlay so
mri_vol2surf would be what I want. Right now, I am just trying to get down the
generic way of how to do it which is why I went with trying to overlay the
parcellation onto the inflated surface. Later, I will have diff
Gotcha, so when I was trying to do something similar I used mri_vol2surf
with --regmethod subjid since you don't actually want to perform a
transformation.
Maybe try that?
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Sep 30, 2016 at 10:54
I am still having problems. If I do --reg subject I get an error back that it
is a directory. If I pick a specific file such as orig.mgz (default according
to help file), I get the same error as before.
Thanks,
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[
Hi Freesurfer expert,
I am doing visual editing.
In some subjects, the pial surface border is somewhat narrow (within the
border of graymatter in my view) although there is no skull stripping
error.
I heard that adding the control point might extend the border of graymatter
as well as that of whit
Did you try --regmethod subjid? or --reg sphere.reg ?
If that doesn't work then I'm not sure how to help - Bruce or Doug, any
thoughts?
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna wrote:
> I am s
Hi there
To my understanding, if you want to edit the pial (push it outwards more)
then you need to edit the white matter, as the pial is made from the white
matter surface. You can do this by manually extending the white matter
surface and re-running your surfaces.
Trisanna
--
Ph.D. Candidate
M
Hi Trisanna,
Thank you for your useful and prompt answer!!
Have a great day.
Best,
Seung-Gul
ᐧ
---
*Seung Gul Kang, M.D., Ph.D. *
*Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical
Center, Gachon University, School of Medicine, 21, Namdong-daero 774
beon-gil, Namdong-gu
Just to make sure I am actually doing what you are suggesting my input and
output is below.
Thanks,
Anna
mri_vol2surf --src
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg
/mnt/netS
hmmm, yup not sure there. Did you try "--regmethod subject"
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna wrote:
> Just to make sure I am actually doing what you are suggesting my input and
> output is below.
Yeah, I get Error: Option unknown for --regmethod
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
[trisanna.sprung-m...@mail.mcgill.ca]
Sent: Friday, September 30, 2016 12:41 PM
To: Free
My apologies, I meant "--regheader subject"
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna wrote:
> Yeah, I get Error: Option unknown for --regmethod
>
> Anna
> --
> *From:* freesur
Thank you! So good news, that worked and created wmparcSlh.w
I'm not sure what the .w means. When I try to load it onto the surface, I get
an error: "Failed to load Surface overlay."
Thank you,
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun..
Ok so this is where my knowledge might be limited because you did a
slightly different thing than me by specifying the output type as "paint" -
that is what the .w format is. This is a label, I believe and needs to be
loaded as such.
What happens if you try to remove the "output_type" and try to l
yes, that's right. You will use mri_vol2surf with the identity matrix
with the parcellation, but some bbregister-generated .dat file with PET
data.
cheers
Bruce
On Fri, 30 Sep 2016, Crawford, Anna wrote:
> No problem. I'm not exactly sure, but I think I just want a surface overlay
> so mri_vol
Hi Seung-Gul
the easiest way to get it to extend further is to play with the intenisty
bounds in mris_make_surfaces. For example, if you reduce
max_gray_at_the_csf_border you will force it to settle further out
cheers
Bruce
On Fri,
30 Sep 2016, Seung Gul Kang wrote:
Hi Freesurfer expert,
that's true, but if the white matter surface is already correct you can
change some of the intensity bounds in mris_make_surfaces. The
automatically calculated ones will be in the recon-all.log and you should
check them before changing them
cheers
Bruce
On Fri, 30 Sep 2016, Trisanna
Sprung
try including --out_type mgh and naming your output something like
lh.wmparc.mgz
cheers
Bruce
On Fri, 30 Sep 2016, Crawford, Anna wrote:
> Thank you! So good news, that worked and created wmparcSlh.w
>
> I'm not sure what the .w means. When I try to load it onto the surface, I
> get an error:
Anna, try removing --out_type paint and instead specify the output file
as wmparcSlh.mgh
Trisanna, thanks so much for chipping in!
On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
> Ok so this is where my knowledge might be limited because you did a
> slightly different thing than me by sp
or better yet, use our naming conventions an dcall it lh.wmparcS.mgh (or
.mgz)
On Fri, 30 Sep 2016, Douglas N Greve wrote:
> Anna, try removing --out_type paint and instead specify the output file
> as wmparcSlh.mgh
>
> Trisanna, thanks so much for chipping in!
>
>
>
> On 09/30/2016 01:14 PM, Tr
Hello FreeSurfer Developers,
We have been testing a dev version of Freesurfer version 6
(freesurfer-Linux-centos4_x86_64-dev-20160405)
Cross-section runs were successful without any error but we have been
getting a segmentation fault error while trying to generate the base
image for longitudinal
First, bring up the ROI on the volume along with the surface in the
volume. You can do this with FreeView. Make sure that the ROI intersects
the surface. Then run mri_vol2surf so sample the binary ROI volume onto
the surface. You can view the ROI on the surface by loading it as an
overlay. Then
You can do the comparison, but the interpretation is difficult. If you
see a difference, how do you know it is not due to the scanner? There's
not much you can do ...
On 09/29/2016 02:54 PM, Martin Juneja wrote:
> Hello FS experts,
>
> I have a data set of 20 subjects (patients) collected at lo
Hi Duygu
V6 isn't ready yet! We are close (I know I keep saying that) and are in
hopefully final internal testing now, but there is no usable version yet.
We'll announce a beta release when it is ready
cheers
Bruce
On Fri, 30 Sep 2016, Duygu Tosun-Turgut wrote:
>
> Hello FreeSurfer Develop
Can you send the mri_coreg terminal output?
On 09/29/2016 11:19 AM, Matthieu Vanhoutte wrote:
> Dear Freesurfer's experts,
>
> I would like to register PET image onto T1 anatomical. I used
> bbregister with the following command and it failed :
> /bbregister --s SUBJID --init-fsl --t2 --mov PET
The pial_avg is an old pial surface created by a previous version of
make_average_surface. Please disregard it.
On 09/29/2016 06:05 AM, A-reum Min wrote:
> Hello experts.
>
> I have some question to you.
>
> I used SurfStat statistical tool to analyze the two group(control,
> patient)
>
> When
There is no such long process for PET. The idea is that you process the
MRI in a longitudinal way, then sample the PET data onto the surface of
the closest MRI time point. Then proceed in a way similar to the
thickness analysis
On 09/29/2016 11:08 AM, Matthieu Vanhoutte wrote:
> Dear Freesurfe
First you need to get an annotation/parcellation of the lobes. You can
try using mri_annotation2label with the --lobesStrict; it may or may not
correspond to what you consider lobes to be. Next you need to run
mri_aparc2aseg specifying your lobes annotation. Look in the
recon-all.log file for a
I can't tell from that image if it is right. Why are you mapping the
wmparc to the surface? The wmparc will have segmentation boundaries
right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
> Thank you everyone for your help! I do
Why not just compute the difference in the lh and rh stats tables? You
don't need to map one hemi to another. But if this is what you want to
do, try looking in the recon-all.log file for the mris_anatomical_stats
command that generates the ?h.aparc.stats
On 09/28/2016 07:42 PM, Ali-Reza Moham
I was just using the wmparc as an example to get a volume overlay onto the
surface. I chose that one just to see the parcellated surface similar to the
volume.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behal
You should use aparc+aseg.mgz and set the --projfrac 0.5. This should
produce something with the same information as the ?h.aparc.annot
(though the color scale will be different)
On 09/30/2016 03:51 PM, Crawford, Anna wrote:
> I was just using the wmparc as an example to get a volume overlay on
I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a
similar type of surface to the one I had sent.
mri_vol2surf --src
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz
--out
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh
examine the actual values. They should be constants that correspond to
the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior
temporal gyrus should be
1030ctx-lh-superiortemporal 140 220 220 0
On 09/30/2016 04:15 PM, Crawford, Anna wrote:
> I did the same thing
There is vertex-for-vertex correspondences, but that does not mean that
each subject aligns perfectly. There maybe some subjects where a vertex
is in the medial wall but not for another subject. They are close, but
not in perfect alignment. What I would do is something like this:
a = [subject1
Hi Douglas,
Does the surface of the closest MRI time point mean the surface of the
-long subject time point directory rather than cross-sectional subject time
point directory ?
Best regards,
Matthieu
Le 30 sept. 2016 9:14 PM, "Douglas N Greve" a
écrit :
> There is no such long process for PET.
Yes
On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote:
>
> Hi Douglas,
>
> Does the surface of the closest MRI time point mean the surface of the
> -long subject time point directory rather than cross-sectional subject
> time point directory ?
>
> Best regards,
> Matthieu
>
>
> Le 30 sept. 2016
Thanks a lot. I'll try this out.
On 09/30/2016 02:00 PM, Douglas N Greve wrote:
> First, bring up the ROI on the volume along with the surface in the
> volume. You can do this with FreeView. Make sure that the ROI intersects
> the surface. Then run mri_vol2surf so sample the binary ROI volume on
I'm not sure where to find the 140 220 220 0, but when I scrolled over what
would seem to be the superior temporal area,I did have a value of 1030 which
changed as I moved to different areas. I added the $h.aparc.annot annotations
to confirm the locations and then compared to the .txt file for a
Right. It is working and the overlay does not look right because of the
color scheme
On 09/30/2016 05:16 PM, Crawford, Anna wrote:
> I'm not sure where to find the 140 220 220 0, but when I scrolled over what
> would seem to be the superior temporal area,I did have a value of 1030 which
> chan
Dear Freesurfer experts
Based on the FS wiki, I calculated the cortical thickness difference between
the LH and RH of a subject in subject's native surface.Now, I want to use FS
commands to extract the information such as "?h.aparc.stats" for this
difference map (LH - RH).Now this difference map
did you see Doug's earlier response to this question?
On Fri, 30 Sep 2016,
Ali-Reza Mohammadi-Nejad wrote:
Dear Freesurfer experts
Based on the FS wiki, I calculated the cortical thickness difference between
the LH and RH of a subject in subject's native surface.
Now, I want to use FS command
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