De : Alain Imaging
Envoyé : lundi 26 septembre 2016 17:17
À : freesurfer@nmr.mgh.harvard.edu
Objet : volume to surface for ROI already in orig space
Hi everyone,
I've used a couple of ROIs that have been drawn in the mni space for
connectivity analysis. Sin
Dear FreeSurfer Developers,
I have the following problem and would be very happy if you could help me. I
have searched the list and did not find the solution to my problem.
I am using FS 5.1 because I have to reanalyze data which I preprocessed in
2014. Back then recon-all and all the group
Dear FreeSurfer Developers,
I have the following problem and would be very happy if you could help me. I
have searched the list and did not find the solution to my problem.
I am using FS 5.1 because I have to reanalyze data which I preprocessed in
2014. Back then recon-all and all the group
Hi,
I keep getting an error when I use mri_label2label. Below is my input and
output. I have tried various paths all the way down to the label and above the
subject level, but still always get the same error. I have also verified it is
the path with the label. Why is it not recognizing it?
Tha
Dear all,
I would like to optimize my design by inserting null-events between my
trials (in order to better catch the HRF shape with reasonable duration of
the experiment) using optseq.
I'm not very familiar with this useful tool and I wonder if you could check
my setup?
Here my design :
I've got
the command should be
[i,j,k] = ind2sub(mri.volsize,pos);
-- Forwarded message --
Date: Tue, 27 Sep 2016 13:00:51 +0700
From: Aziz Nanthaamornphong
Reply-To: Freesurfer support list
To: Freesurfer support list
Subject: Re: [Freesurfer] Coordinates of particular volumes
I have
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that
is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
> Hi,
>
> I keep getting an error when I use mri_label2label. Below is my input and
> output. I have tried various paths all the
Aziz,
Try this:
[i,j,k]=find(mri.vol==17)
and get rid of the ind2sub call
hth
d
On Tue, Sep 27, 2016 at 2:00 AM, Aziz Nanthaamornphong
wrote:
> I have tried to get the coordinates with following commands:
>
> mri = MRIread('aseg.mgz');
> pos = find(mri.vol == 17);
> [i,j,k] = ind2sub(10213,pos
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR
/tools/freesurfer/subjects) which is not where my data is located.
Thanks,
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of D
I think your first argument to ind2sub needs to be size(mri.vol)
cheers
Bruce
On Tue, 27
Sep 2016, Aziz Nanthaamornphong wrote:
I have tried to get the coordinates with following commands:
mri = MRIread('aseg.mgz');
pos = find(mri.vol == 17);
[i,j,k] = ind2sub(10213,pos);
However, I found th
Hi Alain
I believe if you specify the transform as identity.nofile that should do
the trick. Most of our tools accept this
cheers
Bruce
On Tue, 27 Sep 2016, Alain Imaging
wrote:
De : Alain Imaging
Envoyé : l
I also tried doing setenv SUBJECTS_DIR but that did not work either.
bash: setenv: command not found
Thanks,
Anna
From: Crawford, Anna
Sent: Tuesday, September 27, 2016 11:12 AM
To: Freesurfer support list
Subject: RE: [Freesurfer] Co-registering differen
Anna, if you are using bash the command is:
export SUBJECTS_DIR=
On 9/27/16 11:31 AM, Crawford, Anna wrote:
> I also tried doing setenv SUBJECTS_DIR but that did not work either.
>
> bash: setenv: command not found
>
> Thanks,
> Anna
>
> From: Crawford,
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
> Thank you. That worked for changing the default directory. When I run
> mri_label2label, I am still getting the same error that there is no such file
> or directory for the label.
>
> Anna
> ___
Thank you. That worked for changing the default directory. When I run
mri_label2label, I am still getting the same error that there is no such file
or directory for the label.
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.
Hi Bob,
I think freeview by default automatically locates to the default mri
directory under the current subject. It is convenient in some use case
but apparently not so much in your case. I will make that optional or
figure out a better way to handle this.
Best,
Ruopeng
On 9/25/2016 9:46 AM
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label
rh.BA4p.label
aparc.annot.ctab lh.BA45.thresh.labelrh.aparc.a2009s.annot
rh.BA4p.thresh.label
aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot
Hi Freesurfers,
In order to get the better segmentation and surfaces by Freesurfer, do you
think it is necessary to denoise T1 before feed it to Freesurfer? Since
there are several advanced MRI denoising methods which are not covered in
FS preprocessing, I though it would be better to perform one
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/
should be the directory with Test
Hi Zhengchen
I don't think there is a general answer to your question as it depends on
how noisy the input image is, what denoising algorithm you use and what
outcome measures you care about. For example, it might improve
putamen/pallidum but worsen thickness measures in low contrast regions
s
The differences have been found in the outputs from the aseg file.
Particularly, I am interested in the ventricles and the intracranial
volumes. I have loaded both anatomicals in FreeView and toggled between
them and have found no differences visually.
I have attached the files (Via Google Drive s
I have tried multiple variations for my subject directory. I have had it end at
study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or
segfs. I get the same error in all cases still. When using a differnt function
with the subject directory path, I had ended at S2sdt, the
Hi all,
Sorry to re-post:
I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it
(along with some ROIs from FreeSurfer) to the same subject's mprage already
processed (coregistered to functional data) in SPM. To do this, I used:
mri_convert brainmask.mgz brainmask.nii.
Hi,
I'm looking to please get some help with -lgi.
I'm using matlab R2015b and FS5.3 with
recon-all -s subj_id -lgi
on os x 10.11.
Looking at the output, the first error occurs about here:
preparing pial mesh structure ...
...searching for mesh edges...done (206.94 sec).
... creating path fil
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