The problem is solved. Somehow the lh.white file was broken during file
transfer.
2012/5/22 Gabor Perlaki
> Hi all!
>
> I've just ran the preprocessing for TRACULA analysis, with the command
> "trac-all
> -prep -c /home/kutato12/Desktop/dmrirc". It works everything fine, and
> the output files
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Hello everyone,
I guess that this might be a simple question but I couldn't find an
answer to my problem yet.
I would like to extract and visualize four labels from my aseg.mgz
file for illustration purposes. I tried the following:
mri_extract_label aseg.mgz 17 18 53 54 filename.mgz
(the va
Hi all,
I'm trying to analyze a retinotopic mapping dataset using FsFast but some
things don't seem to work the way they should.
When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the following
error:
"ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"
However, I c
> Hi Everyone,
>
> I am new to FreeSurfer, and having some issues with what I believe should be
> a pretty basic operation.
>
> My goal is to register a 4D functional time series to FS average space for
> further connectivity analysis in Matlab (similar to the recent Yeo et al. J
> Neurophy
Hi KK,
mri_vol2surf will take it to individual subject space, then mri_surf2surf
can be used to bring it into average space if you want.
cheers
Bruce
On Thu, 24 May 2012, Kushal Kapse wrote:
>> Hi Everyone,
>>
>> I am new to FreeSurfer, and having some issues with what I believe should be
>>
Hi Martina
you can use mri_binarize --match 17 --match 18... to do this.
cheers
Bruce
On Thu, 24 May
2012, Martina Papmeyer wrote:
> Hello everyone,
>
> I guess that this might be a simple question but I couldn't find an
> answer to my problem yet.
>
> I would like to extract and visualize fo
- Forwarded Message -
From: "Kushal Kapse"
To: "Bruce Fischl"
Sent: Thursday, May 24, 2012 9:14:55 AM
Subject: Re: [Freesurfer] fMRI time series in surface space
hi Bruce,
what if I have .feat files from FSL which have already been processed for
functional analysis..how can i use
Hi Michael, is rtopy.self.lh in the current directory (the one that you
are running selxavg from)?
doug
On 05/24/2012 07:57 AM, Michael Bannert wrote:
> Hi all,
>
> I'm trying to analyze a retinotopic mapping dataset using FsFast but
> some things don't seem to work the way they should.
>
> When
Thanks for your help, Bruce!
Unfortunately, this also leads to a mgz.file where hippocampus and
amygdala are "merged" together so that I can't see anymore what is
hippocampus and what is amygdala (both have same value). I tried some
other things but nothing appears to work. Any other suggestions?
Hi Kushal, if they are already analyzed in FEAT, then you don't need to
sample the time series, just the copes. Alternatively, you can sample
the time series to the surface and analyze it in FEAT as long as you
turn off the temporal whitening. If you want to resample the copes, you
can use reg-
Hi Martina, what exactly do you want? You can get a separate file for
each seg with different calls to mri_binarize specifying only one label.
doug
On 05/24/2012 10:38 AM, Martina Papmeyer wrote:
> Thanks for your help, Bruce!
>
> Unfortunately, this also leads to a mgz.file where hippocampus a
Hi Doug,
thanks for your help.
I need a file with four segmentations being displayed (as outlined
below: left/right amygdala and left/right hippocampus). I know how to
just display ONE segmentation using mri_binarize or mri_extract_label.
However, I need to display ALL of the four and all sh
In that case, use mri_binarize to get a mask of all the segmentations
you want to display, then run mri_mask, something like
mri_mask aseg.mgz mask.mgz aseg-masked.mgz
doug
On 05/24/2012 10:45 AM, Martina Papmeyer wrote:
> Hi Doug,
>
> thanks for your help.
> I need a file with four segmentatio
probably easiest to do in matlab:
[v,M,mr] = load_mgh('aseg.mgz');
ind = find(v ~= 17 & v ~= 53 & v ~= 18 & v ~= 54) ;
v(ind) = zeros(size(ind));
save_mgh(v, 'aseg.mtl.mgz', M,mr);
cheers
Bruce
On Thu, 24 May 2012, Martina Butt wrote:
> Thanks for your help, Bruce!
>
> Unfortunately, this als
amazing! It works - thanks a million :) Martina
Quoting Douglas N Greve on Thu, 24 May
2012 10:56:18 -0400:
> In that case, use mri_binarize to get a mask of all the segmentations
> you want to display, then run mri_mask, something like
>
> mri_mask aseg.mgz mask.mgz aseg-masked.mgz
>
> doug
>
Why not run the full preprocessing? It will do the sampling (and surface
smoothing) for you. Alternatively, you can just use mri_vol2surf, then
mris_fwhm to do the surface smoothing (you can also surface smooth in
mri_vol2surf so you can do it all with one command).
doug
On 05/24/2012 08:35 AM,
Dear all,
I've the following error right after starting trac-all -bedp -c
configuration_file:
Making bedpostx directory structure
Queuing preprocessing stages
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_pre: unexpected operator
[: 486: x: unexpected opera
- Forwarded Message -
From: "Kushal Kapse"
To: "Douglas N Greve"
Sent: Thursday, May 24, 2012 11:45:14 AM
Subject: Re: [Freesurfer] fMRI time series in surface space
run preprocessing of FS-FAST and do sampling on surface seems a good way to
give a tryi am having confusions with d
Hi Gabor,
If you run bedpostX on the data outside of tracula using the default
options, do you get the same error?
Priti
> Dear all,
>
> I've the following error right after starting trac-all -bedp -c
> configuration_file:
>
> Making bedpostx directory structure
> Queuing preprocessing stages
>
Hi, I have a tcl script to save multiple tkmedit screen shots, but I wonder
if there is a way to suppress the pop out tkmedit windows everytime I want
to save the tif.
Basically, if I don't have a X11 window when ssh, how can I save the
tkmedit screen shots with tcl script? Is there an option in tc
Not that I know of. You can try a virtual machine (how I do it), eg
NoMachine or VNC (I prefer NoMachine).
doug
On 05/24/2012 01:59 PM, Natalie Han wrote:
> Hi, I have a tcl script to save multiple tkmedit screen shots, but I
> wonder if there is a way to suppress the pop out tkmedit windows
>
hi,
i am performing feat2surf after i successfully performed
reg-feat2anat...for some reason it gives me "ERROR: cannot find any .img,
.nii, .nii.gz files"although the stats file is in reg folder.may i
please get suggestion on how to proceed from here
thanks
kk
___
Please send the command line and full terminal output.
doug
On 05/24/2012 02:47 PM, Kushal Kapse wrote:
> hi,
>
> i am performing feat2surf after i successfully performed
> reg-feat2anat...for some reason it gives me "ERROR: cannot find any .img,
> .nii, .nii.gz files"although the stats
i got it fixed...thanks
- Original Message -
From: "Douglas N Greve"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, May 24, 2012 2:58:32 PM
Subject: Re: [Freesurfer] feat2surf
Please send the command line and full terminal output.
doug
On 05/24/2012 02:47 PM, Kushal Kapse wrote:
>
Hi Rashmi,
the command line for running the base (subject-template) should be:
recon-all -base AA510 -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all
we usually don't put the '.long' after the base.
I don't think this is causing your problem however. In your case for
some reason the talairach transfor
hello!
in mri_surf2surf, does anyone know how to specify the source and target
formats if --sval is annot without using --sval-annot, as in "--sfmt" or
"--tfmt"?
cheers,
@rno
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mg
Hi Jorge,
in the longitudinal stream all thickness files within each subject are
in correspondence, so it would be sufficient to map all of them
simultaneously (e.g. using the surfaces of the base) to fsaverage.
Should save time and reduce variability.
Also (and this is true for both cross and lo
Dear Priti
The bedpostx works fine on the data if I run it outside of tracula.
The command "/home/kutato12/freesurfer/bin/fsl_sub_seychelles -T 60 -m a -N
bedpostx_pre -l
/home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs
${FSLDIR}/bin/bedpostx_preproc.sh
/home/kutato12/freesurfer/s
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