On Tue, Aug 16, 2011 at 1:42 PM, Leo Souza wrote:
> Does anyone knows how do I run a benchmark test on GPU with FreeSurfer and
> CUDA?
Beyond running a comparison between [x] and [x]_cuda?
If you want numbers on individual routines, then the cudatest
directory holds a lot of test cases which w
Dear Doug,
Thank you very much for your valuable reply.
I still have few questions on which I would like to ask your advise:
QUESTION 1:
While running the recall-all for all my subjects I also used the -qcache
option. I am not sure how this data is further used for my GLM analysis.
I will ap
Dear all,
I have two groups of subjects, and I want to see a difference in
thickness between them controlling for age.
I couldn't find any information in the literature on how the subject's
brains in my groups develop with age. Therefore I can't tell whether
thickness as a function of age for both
Hi Tanja, you should use DODS and test for a difference between the age
slopes of the groups (ie, an interaction between group and age). If
there are no significant interactions, you should then use DOSS to test
for the difference between thicknesses.
doug
Tetiana Dadakova wrote:
> Dear all,
>
Antonella Kis wrote:
> Dear Doug,
>
> Thank you very much for your valuable reply.
>
> I still have few questions on which I would like to ask your advise:
>
> QUESTION 1:
>
> While running the recall-all for all my subjects I also used the
> -qcache option. I am not sure how this data is furthe
Hi Doug,
Thanks again for your help. There are few more things not very clear for me and
I will be very graetful if you can advise me:
1). Did you mean that if I did not qcache my data while I was doing
pre-processing running the recon-all I should use then
lh.AGE.thickness.10B.mgh?
2) Ar
Antonella Kis wrote:
> Hi Doug,
>
>
> Thanks again for your help. There are few more things not very clear
> for me and I will be very graetful if you can advise me:
>
> 1). Did you mean that if I did not qcache my data while I was doing
> pre-processing running the recon-all I should use the
Dear Doug,
Thank you very much! I am ready to start doing my analysis but before I start
you were mentioning that for the simulation 10,000 is a good number. You also
suggested me to run:
mri_glmfit-sim \
--glmdir lh.AGE.glmdir \
--cache 4 neg \
--overwrite
but what is the number of the iterat
for the cache, the simulation has already been done (using 10,000). This
makes it much faster:).
doug
Antonella Kis wrote:
> Dear Doug,
>
> Thank you very much! I am ready to start doing my analysis but before
> I start you were mentioning that for the simulation 10,000 is a good
> number. You
Hi! I successfully run the preprocessing on some polarangle data
(preproc-sess -sf seesid -surface self lhrh -fwhm 5).
Now I would like to do the subtraction between some runs and then to
visualize this subtraction on the surface (so without to analyze the
data with Fourier analysis).
Does anybody
Hi Francesca, can you be more specific about what you want to do? If
you just want to subtract the raw data between runs, you can use fscalc.
doug
francesca strappini wrote:
> Hi! I successfully run the preprocessing on some polarangle data
> (preproc-sess -sf seesid -surface self lhrh -fwhm 5)
I want to verify what's the performance of different GPUs using FreeSurfer as
Benchmark App.
Thanks,
Leo Souza
-Original Message-
From: R Edgar [mailto:freesurfer@gmail.com]
Sent: Wednesday, August 17, 2011 6:20 AM
To: Leo Souza; Freesurfer Mailing List
Cc: Douglas N Greve
Subject:
Dear Doug,
This is my last question for today and I will be very grateful if you can give
me your advise one more time.
When I run the:
mri_glmfit-sim \
--glmdir lh.AGE.glmdir \
--cache 4 neg \
--overwrite
the threshold is 4 (I am not sure why and if it has to be less for example 1.3
as you su
On Wed, Aug 17, 2011 at 3:19 PM, Leo Souza wrote:
> I want to verify what's the performance of different GPUs using FreeSurfer as
> Benchmark App.
In that case, the two best programs to run are
mri_em_register[_cuda] for linear registration
mri_ca_register[_cuda] for nonlinear registration
You
Hi Doug,
Can be the reason that while getting 5 clusters and loading the annotation in
tksurfer shows me nothing because I got the following error?
Could not read annot file
lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot
No such file or directory
ERROR: could not load
lh.age.
Antonella Kis wrote:
> Dear Doug,
>
> This is my last question for today and I will be very grateful if you
> can give me your advise one more time.
> When I run the:
>
> mri_glmfit-sim \
> --glmdir lh.AGE.glmdir \
> --cache 4 neg \
> --overwrite
>
> the threshold is 4 (I am not sure why and if
Use ./lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot
(note the leading "./")
Antonella Kis wrote:
> Hi Doug,
>
> Can be the reason that while getting 5 clusters and loading the
> annotation in tksurfer shows me nothing because I got the following error?
>
>
> Could not read anno
Hello All,
Is there a way to save the outline of a label as an overlay (say .mgh file) ?
Please let me know.
Thanks
Ri
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The inform
Sorry, I try to be more specific.
I would like to be able to take the volume-to-surface transformation
calculated on one set of functional data, and apply that
transformation to another set of functional data (the subtraction) of
the same subject. This will allow me to display arbitrary functional
You can use bbregister to compute the transformation for each run based
on the middle time point of that run (and assuming you've motion
corrected the run), then use mri_vol2surf to resample any data set
aligned with the middle time point to the subject's surface or the
fsaverage surface. You c
You might need to smooth even more.
Michelle Umali wrote:
> Dear Bruce & Doug,
> Thanks I'll do the label comparison.
> I am attaching a fieldsign pic to show the irregularity of the
> blue/red bands. Can you suggest a method of determining V1/2/3 based
> on the odd pattern?
>
> Thank you very
Where may I find the documentation explaining the content and format of the
pial and gray-white surface files? Thanks,
-Jeff
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The inf
This is the polar angle map? What does it look like inflated? Do you
acquire data with the wedge going in both directions? Even if you do,
there can be some delay errors that creep in.
doug
Ritobrato Datta wrote:
> Hello All,
>
> We have processed retinotopy data and piped the phase maps into f
not that I know of. You can convert it to an annotation
(mris_label2annot) and then view the annot in outline mode.
Ritobrato Datta wrote:
> Hello All,
>
> Is there a way to save the outline of a label as an overlay (say .mgh file) ?
>
> Please let me know.
>
> Thanks
>
> Ri
> ___
Can you provide quick instructions on how to run those tests? I am new to
FreeSurfer.
Thanks,
Leo Souza
-Original Message-
From: R Edgar [mailto:freesurfer@gmail.com]
Sent: Wednesday, August 17, 2011 12:36 PM
To: Leo Souza
Cc: Freesurfer Mailing List; Douglas N Greve
Subject: Re: [
Hello-
Trying this post again. I would like to directly compare
asymmetries in FMRI activation in surface space based on the Greve et al
poster presented at HBM this year. We would like to register each subject’s
T1 data to the contralateral hemisphere of fsaverage and made templates o
I don't have any docs set up and ready to use, but here are some
instructions that should get you started.
doug
---
Download these files
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre
Thanks a lot!
I tried the registration with bbregister but unfortunately when I checked
the result the functional volume was very distant from the target.
Could I tried something else to improve the registration?
I typed:
bbregister --s subject --mov name_file.nii --reg register.dat --init-fsl
--
It was probably the initialization that failed. To test this, run
fslregister (very similar command line to bbregister). If that does not
look good, then it is an init problem. If these were acquired in the
same session, then you can try using --init-header. If you have spm
installed, you can t
Hi Jeff,
Not sure where you can find a verbose documentation, but you can figure
out by looking at the file read_surf.m in the ${FREESURFER_HOME}/matlab
directory. It's straightforward.
All the best,
Anderson
On 08/17/2011 04:32 PM, Jeff Eriksen wrote:
Where may I find the documentation expla
Hi all - By popular demand we've posted the dmri_* executables compiled on
snow leopard here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
This is not the entire FS distribution, just the commands that are called
by trac-all. If
self-documenting code :)
On Wed, 17 Aug 2011, Anderson Winkler wrote:
Hi Jeff,
Not sure where you can find a verbose documentation, but you can figure out
by looking at the file read_surf.m in the ${FREESURFER_HOME}/matlab
directory. It's straightforward.
All the best,
Anderson
On 08/17/2011 0
Hello,
I'm trying to install FreeSurfer
(freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) on an
Ubuntu-10.04 x86_64 AMI hosted on Amazon's EC2, but after following the
installation instructions I am unable to complete the "Testing your
Freesurfer Installation" section. I am not trying to
i havent seen this problem. i think others have run freesurfer on the
amazon cloud before.
the only thing i can think of, when you mention that the mri_* tools
will not run (and in the recon-all.log, only the scripts printed their
version info) is that the mri_* executables are all run through th
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