Hi Experts,
I just wanted confirm my understanding that Freesurfer does not employ
multi-atlas label fusion methods. Is this correct?
Thanks,
Best,
Joshua
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
__
Hi, Eugenio
Just noticed the first lines of aseg.stats. From the command line
recon-all pipeline uses to make the original aseg.stats file it uses
norm.mgz so I think it is the best file to use for intensity comparisons
like I proposed.
Thank you.
Marcos
Em Qua, 2013-06-12 às 13:33 -0300, Marcos M
Good idea. Actually, I need to fix selxavg3-sess to handle this
better. When I wrote it, I never tested it on runs with so many time
points, but they are becoming more common.
doug
On 6/13/13 5:26 PM, Marcel Falkiewicz
wrote:
You will need to make sure it is executable by running
chmod a+x optseq2
You then need to put it in your path, rehash, and it should run.
Also, if you have freesurfer installed, then it should be there already
doug
On 6/13/13 5:10 PM, fMRI wrote:
> Hi all,
>
> I am trying to install optseq2 in
Thanks Jacek for the advice, I'll try to upgrade to newer MATLAB version,
maybe it will manage the memory better. I've got 64 bit versions of
everything, so this doesn't really help. I've never considered a 800
timepoint timeseries as a large dataset, other software packages do not
seem to be bothe
Hi all,
I am trying to install optseq2 in my own laptop. I have linux installed as a
virtual window.
I am sorry but I really do not have any idea how I should install it after
downloading the file. I am new to linux!
Any guide please,
Thanks
AS
___
No, no difference
doug
On 6/13/13 3:56 PM, Reza Rajimehr wrote:
> ... and one more question:
>
> In the latest version of FS-FAST (v5.3), is there a difference between the
> following two:
>
> mkcontrast-sess -analysis whatever -contrast 1vsFix -a 1 -c 0
>
> mkcontrast-sess -analysis whatever -co
In that case, you could break it up in to several shorter runs. It won't
affect the stats much (probably help it), but it does make it a little
more difficult to set up the data. If you want to do this, you would
need to do something like this:
cd session/bold
mv 001 001.big--> m
It is not a matlab problem per se, though their memory management is not
great. This sometimes happens for the mni305 when you have a lot of time
points in one run or many runs. How many runs and how many time points
per run? And you are doing 2mm (the default) or 1mm?
doug
On 6/13/13 2
... and one more question:
In the latest version of FS-FAST (v5.3), is there a difference between the
following two:
mkcontrast-sess -analysis whatever -contrast 1vsFix -a 1 -c 0
mkcontrast-sess -analysis whatever -contrast 1vsFix -a 1
I have blocks with no stimulus that I have specified them
Hello,
I know this problem has been discussed earlier, but I think in my case the
source of the problem might be quite different. I'm running FS 5.3.0 and
MATLAB R2011a on Ubuntu machine with 12 GB RAM. selxavg3-sess runs
perfectly for both hemis, but I get the following error when trying to run
i
Hi Daria, this is not something you would do with tkregister. First, you
need to map the curvature from the individual subject to fsaverage_sym.
You can do this for all subjects in your group with a call to
mris_preproc; spec --meas curv instead of --meas thickness. Then load
this as an overla
Hi Doug,
I've tried using tkregister2 and registering my individual subject's T1 to the
fsaverage_sym but it hasn't worked. Could you point me to the correct movable
volume and register.dat files that I should use? I'm not sure what they print
out as.
Thank you,
Daria
___
Hi Prapti, can you send the full terminal output? The ill-conditioned
error is probably not related to the contrast. It is usually related to
the design matrix, which makes it difficult to track down because you
will have a different one at each vertex with --pvr.
doug
On 6/13/13 1:14 PM, Ga
Dear FreeSurfers
I am trying to control for thickness in another surface using the pvr option in
mri_glmfit. However, I'm confused as to how I can include the pvr option
correctly in the contrast files.
I have two groups, and would like to utilize DODS for this analyses as I think
that my group
Did it change anything at all? Make a copy of the talairach.xfm file,
re-run, and see if it is different in any way.
doug
On 6/13/13 1:06 PM, Peter Boulos wrote:
Hi Doug,
I am using a GE 3T scanner with a slice thickness of 1.7 mm. I tried
using the new script you provided (thanks for the he
or you can convert the label to a mask, then run mri_mask on he
sig.nii.gz file, then view it in tksurfer. Bruce's suggestion is
probably easier.
doug
On 6/13/13 1:04 PM, Bruce Fischl wrote:
> Hi Resa
>
> you can create a label of the region you are interested in and use the
> mask_label comman
Hi Resa
you can create a label of the region you are interested in and use the
mask_label command on the tcl prompt when running tksurfer.
cheers
Bruce
On Thu, 13 Jun 2013, Reza Rajimehr wrote:
> Hi,
>
> Using anatomical parcellation, I have labels for the occipital and
> temporal lobes in my
Hi Pedro,
about your first question:
call the recon-all -long command exactly as you would do the processing, but
instead of -all pass -localGI
No idea about 2).
Best, Martin
On Jun 13, 2013, at 12:02 PM, Pedro Rosa wrote:
> Dear all,
> I have two issues:
> 1) I would like to run localGI in
Dear all,
I have two issues:
1) I would like to run localGI in a longitudinal analysis. I runned the
recon-all, the -base and the -long in all subjects. Then, I tried to run the
-localGI command on .long. directories (I believe this it the directory I
should run the command), the error below re
Hi,
Using anatomical parcellation, I have labels for the occipital and
temporal lobes in my subject. I have a functional map in the same subject
that I want to show the activity only in the occipital and temporal
cortex, and I want to mask the activity in the other parts of the cortical
surface. H
Does that file exist? Do you have permissions?
doug
On 6/12/13 12:59 PM, Sudhin A. Shah wrote:
Hi,
recon-all was successful.
But when I try
reg-feat2anat --feat '/home//func/2_reg' --subject xyz
I get an error with
MRISread(/home/sudhin/Data/freesurfer_subjects//xyz/surf/lh.white):
c
you have to chose it yourself
doug
On 6/13/13 6:04 AM, Anupa AV wrote:
Dear FS experts,
By definition bblabel means..
Applies a bounding box to a label. The bounding box is specified by
six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label
points within this box are copied to the
On 6/13/13 9:45 AM, A a wrote:
Hello all,
A question regarding the usage of Optseq2
I have this command line
optseq2 --ntp 200 --tr 2.5 --psdwin 0 15 2.5 --ev ev20 2.5 20 --ev
ev40 2.5 20 --ev ev60 2.5 20 --tnullmin 5 --tnullmax 7.5 --nkeep 1 --o
OptSeq_TRIALS/3_null9_6 --nsearch 1
No
Hello all,
A question regarding the usage of Optseq2
I have this command line
optseq2 --ntp 200 --tr 2.5 --psdwin 0 15 2.5 --ev ev20 2.5 20 --ev ev40 2.5
20 --ev ev60 2.5 20 --tnullmin 5 --tnullmax 7.5 --nkeep 1 --o
OptSeq_TRIALS/3_null9_6 --nsearch 1
Now the efficiency tha I get is around
Hi Lucy
recon-all -i -s \
-sd -all
should do the trick
Bruce
On Thu, 13
Jun 2013, wrote:
Hi expert,
How can I segment the white matter,gray matter and the cerebral hemisphere
,and rebuild the surface?
Thanks in advance,
Best wishes,
lucy
__
Hi expert,
How can I segment the white matter,gray matter and the cerebral hemisphere ,and
rebuild the surface?
Thanks in advance,
Best wishes,
lucy___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard
Dear FS experts,
By definition bblabel means..
Applies a bounding box to a label. The bounding box is specified by
six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label
points within this box are copied to the output. If a min is not
specified, then -infinity is used. If a max is not
PS: Which files/folders will I need to delete after I'll have fixed the
problem, before re-running the recon? Or will it just overwrite any
left-overs?
On 13 June 2013 10:32, Tudor Popescu wrote:
> Hi all,
>
> The command:
>
> recon-all -s M19 -localGI
>
> resulted in:
>
> make_outer_surface('/m
Hi all,
The command:
recon-all -s M19 -localGI
resulted in:
make_outer_surface('/media/math/all38subj/M19/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/media/math/all38subj/M19/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=
ERROR:: Too many arguments.
I
Thanks again for the answers, I have now got it working. It was my
fault, I thought the name should be libcrypt.so and not as I found out
it should be libcrypt.so.1.
So the solution for OpenSUSE 12.3 (64 bit) is to copy e.g.
/lib64/libcrypt-2.14.1.so from an OpenSUSE 12.1 installation to
/lib
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