Dear freesurfer experts,
I am currently do group analysis in qdec, and I canot select jacobian white
from the drop down menu, I thought this would be an option? Do I do have
additional steps to get these values?
Kind Regards,
Linn
___
Freesurfer
Hi
i used freesurfer labels in a study and i want to identify the broadmann
areas corresponding to some labels, is there any correspondence between the two
?
Thanks
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hi all,
When I run selxavg3-sess for any analysis, the following information is
always appearing. Can you please give some suggestions how to fix that? Any
thoughts would be very appreciated!
--
--- matlab output
Warning:
Hi Albert
that sounds pretty mysterious and probably some left-over debugging code
that you somehow activated. Can you check to make sure that you don't
have an environment variable named DIAG defined? And what do the various
Ns run from and too (that is, what are the names of the files)? Any
Hi Laouchedi
that is a big research question! The answer is a qualified yes, but it
depends strongly on what labels you mean. In general we find that the
closer you are to primary areas like V1/M1, the stronger the correspondence
is. We do supply some explicit estimates of Brodmann areas,
hi bruce,
related to this question, how are the stats/volumes of the BAs computed?
cheers,
satra
On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Laouchedi
that is a big research question! The answer is a qualified yes, but it
depends strongly on what
Hi Satra,
what version are you using? I think Anastasia implemented a thresholded
version in 5.3, but perhaps she can comment.
Bruce
On Fri, 26 Jul 2013, Satrajit
Ghosh wrote:
hi bruce,
related to this question, how are the stats/volumes of the BAs computed?
cheers,
satra
On Fri, Jul
hi bruce,
currently 5.3, but the data i was looking at was processed with 5.1 and in
that right ba44/45 was always larger.
cheers,
satra
On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Satra,
what version are you using? I think Anastasia implemented a
if it's not the thresholded version that might reflect the fact that it
is less well-predicted and so the borders are more spread out
Bruce
On Fri, 26 Jul
2013, Satrajit Ghosh wrote:
hi bruce,
currently 5.3, but the data i was looking at was processed with 5.1 and in
that right ba44/45 was
Hi
thank you for the reply. Yes, i have looked at them, in fact i used the
freesurfer parcels as nodes in a TBI connectivity study and i want to report my
results both in terms of the freesurfer components and broadmann areas. i just
asked, if since, some probabilistic map of broadmann
those are the probabilistic estimates of the Brodmann areas (that is, the
files in the label dir named h.BA*.label)
cheers
Bruce
On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
Hi
thank you for the reply. Yes, i have looked at them, in fact i used the
freesurfer parcels as nodes in a TBI
There is a *.thresh.label version of all the BA labels in 5.3, but I don't
think it's used by default. You can try using those labels instead.
On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
hi bruce,
currently 5.3, but the data i was looking at was processed with 5.1 and in
that right ba44/45
thanks guys. any thoughts on when the ba*.stats files will use these? right
now i agree with bruce that they are biased by the predictability of the
region. less accurate prediction - greater volume.
cheers,
satra
On Fri, Jul 26, 2013 at 10:28 AM, Anastasia Yendiki
Hello Doug,
I am encountering the error below when running spmregister. Where do you
think is the issue? Thanks!
Best,
Marco
bash-4.1$ spmregister --mov $file.nii --s PBR_$subj --reg tmp.dat
--fsvol merged.lrrev
Log file is ./spmregister.log
Fri Jul 26 10:52:49 EDT 2013
--mov
Hi again,
interestingly, if I run the same command using the full fsvol path I get
the 'Disk quota exceeded' message... I wonder if even the message I wrote
you about in my previous email has something to do with disk space.
I will try free up some room and try spmregister again!
Marco
You can search recon-all.log for the command that generates those stats
and appply it to the ?h.BA.thresh.annot instead of ?h.BA.annot.
On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
thanks guys. any thoughts on when the ba*.stats files will use these? right
now i agree with bruce that they are
Hi Doug and Bruce,
When I am running mri_binarize with aseg.mgz as input and --match 77 I get
clusters, but when I run the same thing with the orig.mgz as input, I get
individual voxels and not any clusters are forming. Could you please explain to
me why is this happening and whether there is
Hi Panos
when you run it with the orig you are getting voxels that happen to have
an intensity of 77 and have nothing to do with lesions. Run it on the
aseg
Bruce
On Fri, 26 Jul 2013, Fotiadis, Panagiotis wrote:
Hi Doug and Bruce,
When I am running mri_binarize with aseg.mgz as input and
Hi Bruce,
I see. In that case, do you happen to know if there is another way to get
clusters with orig as the input? Maybe by setting a threshold instead of a
match?
Thanks again,
Panos
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, July
That probably just means that you have run out of space in the directory
you are running it from. Run
quota -v
to see
doug
On 7/26/13 11:27 AM, Marco Loggia wrote:
Hi again,
interestingly, if I run the same command using the full fsvol path I get
the 'Disk quota exceeded' message... I
no, segmenting lesions is hard and can't be done with a simple threshold
On
Fri, 26 Jul 2013, Fotiadis, Panagiotis wrote:
Hi Bruce,
I see. In that case, do you happen to know if there is another way to get
clusters with orig as the input? Maybe by setting a threshold instead of a
match?
what version of spm are you using? Look in your ~/matlab/startup.m file
to see. If you are using version 5 or less, then add --img
doug
On 7/26/13 11:19 AM, Marco Loggia wrote:
Hello Doug,
I am encountering the error below when running spmregister. Where do you
think is the issue? Thanks!
Hello Freesurfer Experts,
We would like to use PySurfer's function plot_label_foci.py to
automatically create circular labels of a pre-defined radius (eg. 14mm) on
the fsaverage surface of freesurfer.
What are the specified units of n_steps in the command line argument
Hi Linn, what do you mean that you cannot select it? Is it grayed out?
doug
On 7/26/13 4:20 AM, Linn Mittlestein wrote:
Dear freesurfer experts,
I am currently do group analysis in qdec, and I canot select jacobian
white from the drop down menu, I thought this would be an option? Do I
do
Ok, thanks for your reply!
Best,
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, July 26, 2013 12:35 PM
To: Fotiadis, Panagiotis
Cc:
Hi James, does everything run to completion? If so, then you can ignore
those warnings.
doug
On 7/26/13 8:35 AM, Wang Zhiwei wrote:
Hi all,
When I run selxavg3-sess for any analysis, the following information
is always appearing. Can you please give some suggestions how to fix
that? Any
yes, use isxconcat-sess (after you have done the 1st level analysis of
course). To use the r-rvalue, add -m pcc to the isxconcat-sess command
line
doug
On 7/25/13 1:54 PM, Mario Ortega wrote:
Hi Team,
I have a question on making a group average of subjects for functional
connectivity.
Hello,
I have another newbie question. I'm running qdec, trying to compare cortical
thickness in children with and without ADHD. However, I'm seeing a discrepancy
between the clusters that are significant according to the terminal (after
applying the Monte-Carlo simulation with default
Hi Maria, can you tar up the qdec output folder and send it to our file
drop? I'm traveling now, so it might be the 1st week of august before I
can take a look. You can also go into the qdec output folder and run
tksurfer to show you the results.
doug
On 7/26/13 1:37 PM, Maria Kharitonova
hi sarah,
you'll get a much quicker response posting PySurfer related questions to:
nipy-de...@neuroimaging.scipy.org
cheers,
satra
On Fri, Jul 26, 2013 at 12:57 PM, sar...@nmr.mgh.harvard.edu wrote:
Hello Freesurfer Experts,
We would like to use PySurfer's function plot_label_foci.py to
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