Hi Dr. Greve,
Thanks for your reply.
Could you please confirm once recon-all -all is done, following steps are
correct to get cortical thickness, volume and area stats using Yeo atlas:
(1). Use "-sval-annot" option to transfer annotation (Ref.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurf
It is the first frame. You'll have to get the average from the
gtm.nii.gz file. You can do it easily enough in matlab with
gtm = fast_vol2mat(MRIread('gtm.nii.gz'));
% gtm will be a 4xNrois matrix
mean(gtm)
On 12/09/2016 03:21 AM, Donatas Sederevicius wrote:
>
> Hello FreeSurfer Developers,
>
recon-all all will register the two together and reslice the flair into
the conformed space, so you should not have to worry about it
On 12/14/2016 06:23 PM, Octavian Lie wrote:
> Dear All,
>
> Our MPRAGE and T2 SPACE FLAIR sequences are acquired at times during
> two different scans, and the M
You will need to create the yeo parcellation for each subject as well as
run mris_anatomical_stats to create the stats file, then run
aparcstats2table specifying the new stats file. Look in the
recon-all.log file to see how to call mris_anatomical_stats
On 12/14/2016 03:56 PM, Martin Juneja wr
You need to open the fsaverage surface using tksurfer or freeview, then
find a vertex in the location where you want to create the label, then
get the vertex number and replace "vertexno" in the command with that number
On 12/14/2016 02:54 PM, Leyton Moscoso, Cristian Eduardo wrote:
> Hi Dou,
>
Dear All,
Our MPRAGE and T2 SPACE FLAIR sequences are acquired at times during two
different scans, and the MPRAGE seq further gets reoriented in a pipeline
upstream of the Freesurfer step.
For best results, does the FLAIR volume have to be reoriented (and
resliced) in a rigid registration to the
We are shooting for Wed Dec 21 for a final release of v6, so you may
want to use that. If you run recon-all on a data set that has already
been edited, it will use the edits you have (and will not delete them),
so I recommend making a backup of your 5.1 analysis and then run 6.0 on it.
On 12/1
Hi All, as you finalize your OHBM abstract, remember to cite FreeSurfer.
There is a box to check that you used FreeSurfer when you submit your
abstract, but also please put some indication in the text that you used
FreeSurfer if you can. If you have room to put in a citation, there are
several
Hi Tamara,
first you need to make sure that this is not just a viewing setting, so in
freeview copy the brightness setting to all inputs (there is buttons for that,
like copy setting and apply to all, underneath the list of images).
If you still see differences, check the original inputs. If
Hi Allison,
you have two options:
1. replace the mri_robust_register and mri_robust_template executables with
newer ones (but who knows if flags changed, so this may not work directly, in
that case also the call in recon-all may need to be adjusted).
2. better: simply run all bases with 5.3
Hi Matthieu,
1. yes, LME needs to be done first so that values can be sampled from the
fitted model for the SA.
2. yes, I was talking about gradient non-linearities etc that could be in the
image from the acquisition. We currently don’t use non-linear registration
across time points (only rigi
Hi Bruce,
Running -autorecon2 -autorecon3 did not seem to fix the surfaces for this
subject. Do you have any further suggestions on what we could try to correct
the surfaces?
Thank you!
Batool
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-b
Hi,
I would like to use aparcstats2table command. By default, it uses
Killiany/Desikan
parcellation atlas. But I would like to use atlas by Yeo and colleagues (
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011).
Could you please let me know how can I use this atlas instead
Hi Dou,
I have had some issues with running mri_volsynth.
It is not clear how to specify the coordinate for the selected vertex. I tried
it by adding the flag --c_ras x y z, but did not work?
Thanks
Cris
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesur
Ohkay thanks, we'll go ahead and run autorecon2 and autorecon 3 on this subject
then.
Thanks!
Batool
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Wedn
Hi Batool
if you need to change the watershed you will need to rerun everything
from there forward. All of autorecon2 and autorecon3 I think at least
cheers
Bruce
On
Wed, 14 Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
We have a subject on which we had to do adjust the water
André,
It looks like you have the matlab path typed correctly. I would try to
tab complete it in a terminal to check.
You currently have it typed as this:
/Applications/matlab/MATLAB_R2014a.app/bin/matlab
I expect it to be this on your computer:
/Applications/MATLAB_R2014a.app/bin/matlab
Try doin
Or more precisely (sorry for all the emails):
Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));
Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);
Error in reorganize_verticeslist (line 28)
[nextindex,nextvalue]=mesh_vertex_nearest(mesh_
Finally, I was able to add the path:
export PATH=$PATH:/Applications/matlab/MATLAB_R2014a.app/bin/
Unfortunately, I receive a new error:
ERROR: make_roi_paths did not complete successfully!
Do you know what happened now? To compute LGI, I just use the rh.pial and
lh.pial from recon-all all (on
I get the following:
Andres-MacBook-Pro:subjects andre$ getmatlab
ERROR: Cannot find matlab.
Does not exist or is not in path.
I guess adding the path (or what I defined as path) didn't work.
Bw
André
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesur
What happens if you run getmatlab ?
On 12/14/16 7:14 AM, André Schmidt wrote:
Dear Doug
Thanks again for your help. I think I have added the path to my linux
path. This is what I have done:
Andres-MacBook-Pro:~ andre$ echo $PATH
/Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/l
Dear FS experts,
We are planning to update all our subjects from de 5.1v to 5.3v. Our subject
database processed with the 5.1v is really big so we are thinking about ways to
not start over new. Is there any way to take advantage of the 5.1v
segmentations? We have been thinking about using a dil
Hi Aya
no, you can either have it be 256^3 or specify -cm and it will make an
isotropic output with the smallest input resolution
cheers
Bruce
On Wed, 14 Dec 2016, Aya
Kabbara wrote:
Dear freesurfer team,
Do we have the option when using "recon-all" command to predefine the
dimensions o
Dear FreeSurfers,
Thanks for the previous reply on what the white.K and white.H are.
I would like to make an analysis in Qdec using one of these measures.
However, I didn't find much information online so I would like to ask you 3
final things:
1. Which of the two measures (mean, gaussian) is mor
Dear Doug
Thanks again for your help. I think I have added the path to my linux path.
This is what I have done:
Andres-MacBook-Pro:~ andre$ echo $PATH
/Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin
Andres-MacBook-Pro:~ andre$
PATH=/Applications/fsl/fsl/bin:/
Dear freesurfer team,
Do we have the option when using "recon-all" command to predefine the
dimensions of the segmented MRI? (for example 145*174*145 with 1.25 mm).
Thank you a lot,
Aya
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