--- Begin Message ---
Hi,I'm wondering whether the FS-FAST performed bandpass filtering.
Stefano___
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Dear Experts,
I am currently working with the non-linear FreeSurfer normalization.
We have a small group of subjects N = 12 and in each brain we
identified a single position with a fMRI localizer. The task is a
group comparison of the individual results for this position.
Therefore, the coordi
Hi pfannmoe
that page looks pretty good to me. YOu need to create a new folding atlas
which we typically store in .tif format using mris_make_template. This is
usually done by picking one subject, registering all your subjects to that
template (.tif file), recreating the template, reregistering
Hi Freesurfer
I'm struggling with trying to edit the scale bar in tksurfer. Commands like
'set scalebar_bright 240' work, but draw_scalebar gives an invalid command
error.
I've tried redrawing, but it doesn't help.
Basically, I want the black background to become white (can do it via convert
-
Hi Michael
tksurfer is deprecated - have you tried this in freeview?
cheers
Bruce
On Fri, 1 Apr
2016, Michael Asghar wrote:
Hi Freesurfer
I’m struggling with trying to edit the scale bar in tksurfer. Commands like
‘set scalebar_bright 240’ work, but draw_scalebar gives an invalid comman
Oh, I didn’t know that. I've been advised to use tksurfer (we're trying to get
nice images of PET data overlaid on surfaces).
I haven't got a clue how to use freeview - any simple commands to load up a
surface, overlay some statistical data?
Thanks!
Michael
-Original Message-
From: fre
freeview -f lh.inflated:overlay=lh.pet_data.mgz
would be a good place to start. There's lots of stuff on the wiki
cheers
Bruce
On Fri, 1 Apr 2016, Michael
Asghar wrote:
Oh, I didn’t know that. I've been advised to use tksurfer (we're trying to get
nice images of PET data overlaid on surf
Thanks
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 01 April 2016 14:58
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer scale bar
freeview -f lh.inflated:overlay=lh.pet_data
Hi again
I think I've figured out how freeview works, but I'm having trouble loading
functional data taken from SPM12, and overlaying it on a surface in freesurfer.
I can load the lh.inflated and also load the spmT.nii file, but I'm just
getting a grey surface, and playing with the scale doesn't
Dear Freesurfer Experts,
I have run my participants' longitudinal sMRI data through the
preprocessing longitudinal pipeline, ran the LME multivariate analysis,
cluster-thresholded the data, and am now trying to visualize those results
in Freeview (for some reason tksurfer is very, very slow to run
Hi Emad - The error happens at the very beginning, so I'm wondering if
something went wrong in the previous steps, before -path. Can you please
send me the entire trac-all.log of one of your subjects? Thank you!
a.y
On Wed, 30 Mar 2016, Emad Ahmadi wrote:
Hi Anastasia,
I hope you’re enjoy
you can also try tksurferfv. this is a frontend for freeview that takes
tksurfer-style arguments
On 04/01/2016 09:57 AM, Bruce Fischl wrote:
>
> freeview -f lh.inflated:overlay=lh.pet_data.mgz
>
> would be a good place to start. There's lots of stuff on the wiki
> cheers
> Bruce
>
>
>
> On Fri, 1
is the spm data mapped to the surface (with mri_vol2surf) or a volume?
On
Fri, 1 Apr 2016, Michael Asghar wrote:
Hi again
I think I've figured out how freeview works, but I'm having trouble loading
functional data taken from SPM12, and overlaying it on a surface in freesurfer.
I can load the
You can put surface data back into the volume with mri_surf2vol (which
will also merge left and right into one volume). What do you do with the
aseg data?
On 04/01/2016 10:46 AM, Jennifer Legault wrote:
> Dear Freesurfer Experts,
>
> I have run my participants' longitudinal sMRI data through the
Thanks for your help - I'll look into it and let you know if I have problems
Michael
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 01 April 2016 16:19
To: freesurfer@nmr.mgh.harvard.edu
S
Hi Doug,
I'm trying to map a cortical label onto the surface (i.e. extract a nifti file
for a particular label). So instead of a label.label file, it's a label.nii
that I can load in as an overlay in, say, tksurfer. Is there a way to do this
using freesurfer commands?
___
Use mri_label2label specifying the source and target subjects to be the
same, a regmethod as surface, and select the --outmask option
On 04/01/2016 11:37 AM, Afzal, Afsana wrote:
> Hi Doug,
>
> I'm trying to map a cortical label onto the surface (i.e. extract a nifti
> file for a particular labe
Not by default, look at mkanalysis-sess -help for more details,
especially the -hpc and -lpc options.
Hi,
I'm wondering whether the FS-FAST performed bandpass filtering.
Stefano
On 04/01/2016 03:11 AM, std...@virgilio.it wrote:
>
>
>
> ___
> Freesur
Hi Sneha,
looks like an IO problem, maybe the disk is full or the mount was broken?
Strange that is reports finished without error, when in fact there are
many errors (if you scroll up you can see many 'file not found'
messages). Anyway. This is 5.1 and very old. I would recommend to check
th
Hi Martin,
Yes, I indeed checked the log file and saw so many errors, and was therefore
very surprised as to how did it run through the pipeline without any error
message. Thank you so much. I shall look at the specs for the disk space and
notify if something unusual occurs. But its strange th
Hi Sneha,
Yes, mixing versions could also produce problems. 5.1 works in native
spaces all the way trough to the long runs, while 5.3 works in the base
space for the long runs. Don't mix versions.
Best, Martin
On 04/01/2016 12:38 PM, Sneha Pandya wrote:
Hi Martin,
Yes, I indeed checked
Are there any labeled nifti atlases that correspond to the freesurfer
parcellation atlases output from recon-all?
I'm basically interested in visualization of group results.
-Greg
___
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Hi Emad - I believe that it's not finding your freesurfer recons. They
should be under the $SUBJECTS_DIR and have the same names for time points
and longitudinal template as what is under your tracula output directory
(if the latter is different from SUBJECTS_DIR).
Best,
a.y
On Fri, 1 Apr 2
That works perfectly, thank you!
__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
_
do you want it in the volume or the surface? In the volume, there should
be a file called $FREESURFER_HOME/subjects/fsaverage/mri/aparc+aseg.mgz
you can convert that to nifti
On 04/01/2016 02:20 PM, Gregory Book wrote:
> Are there any labeled nifti atlases that correspond to the freesurfer
> par
Hi Doug,
Thanks for your quick response! When running the LME mass univariate
analysis, I am assuming this also includes subcortical structures,
correct? From my understanding, subcortical areas are segmented as opposed
to parcellated. The main thing I want to examine all the regions of the
bra
recently download and trying the dev version of freesurfer 6.
it exited with this error
#@# Cortical Parc 2 lh Fri Apr 1 13:41:04 AEDT 2016
/usr/local/freesurfer6/subjects/test/scripts
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz
-seed 1234 testphp lh ../surf/lh.sphe
yes, that is fixed now
Bruce
On Sat, 2 Apr 2016, Nathan Malitz wrote:
recently download and trying the dev version of freesurfer 6.
it exited with this error
#@# Cortical Parc 2 lh Fri Apr 1 13:41:04 AEDT 2016
/usr/local/freesurfer6/subjects/test/scripts
mris_ca_label -l ../label/lh.cortex.
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