Hello all,
What is the mean curv in the stats files a measure of?
Thanks kindly,
Vina
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Hi,
I'm Francisco Robles, from México city. I am using FS-Fast to analyze some
event-related fMRI. My problem is jow to use the paradigm file because I need
to exclude some images from my analysis. The situation is that I have a
paradigm of 3.5 secs of stimulus and a variable quantity of Null/
Hello,
Does the frame flag refer to offsets? If so, would frame 5 be the same as
offset 5 (6 seconds)?
Thank you,
Dave Brohawn
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basically, yes. It is the 0-based frame number. The time of this frame
will depend on your TR and prestim.
doug
Dave Brohawn wrote:
Hello,
Does the frame flag refer to offsets? If so, would frame 5 be the same as
offset 5 (6 seconds)?
Thank you,
Dave Brohawn
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Try running it with --no-vol. If you don't have this option, then you
may need to upgrade.
Ruchika Shaurya Prakash wrote:
Hello
I am running the make_average script on 92 Ss and get the following error
message:
nframestat = 92
Allocating output
mri_concat (63810) malloc: *** mmap(size=2621
I do have this option - but that would mean that I would not get the
average for volumes?
Also, if you take a look at the make_average_surface.log - that got
completed without any problems. So do I need to run the
make_average_subject command again?
Thanks,
-Ruchika.
On Jan 27, 2009, at
Sorry, just run it with --no-aseg (for that you may need a new version).
It probably ran the surfaces ok and then bonked on the volumes (and
probably only on the aseg).
doug
Ruchika Shaurya Prakash wrote:
I do have this option - but that would mean that I would not get the
average for volumes
I don't think you'll need to run the surfaces again. --no-aseg is passed
to make_average_volume from make_average_subject.
Ruchika Shaurya Prakash wrote:
I just downloaded the latest version last week. Is there a change since then?
Also, I get the --no-aseg option with make_average_volume and
I just downloaded the latest version last week. Is there a change
since then?
Also, I get the --no-aseg option with make_average_volume and not with
make_average_subject - but I am thinking that is probably okay since
the surfaces are already done. Do you think that I need to run the
surfac
Hi,
I am attempting to run the following command:
preproc-sess -s CD_R01BTX_ctrl1_sess1 -df sessdirfile -mcout fmc5 -fwhm 5
-smin fmc5 -smout fmcsm5
and am getting an error:
>>>Tue Jan 27 16:33:44 EST 2009
>>>mcparams2exterg: finished
>>>\n\n
>>>Tue Jan 27 16:33:44 EST 2009
>>>mc-sess complete
what version of freesurfer?
j...@nmr.mgh.harvard.edu wrote:
Hi,
I am attempting to run the following command:
preproc-sess -s CD_R01BTX_ctrl1_sess1 -df sessdirfile -mcout fmc5 -fwhm 5
-smin fmc5 -smout fmcsm5
and am getting an error:
Tue Jan 27 16:33:44 EST 2009
mcparams2exterg: finish
The mean curvature for that particular parcellation.
There is a slide demonstrating curvature here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ArticlesSlidesAndPosters
Under the Slides section, the one called "Anatomical Analysis with
FreeSurfer". It's slide #14.
--
On Tue, 27 Jan 2009, Vina
Hi,
I am analyzing my fMRI data and I got a memory alloc problem in "mri_fwhm"
The exact message is :
mri_fwhm --mask
/tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i
/tmp/sk/FSFAST/abe_090116/bold/VisualActivations/res/all.nii --sum
/tmp/sk/FSFAST/abe_090116/bold/VisualActivatio
how big is all.nii and how much memory do you have on that computer?
Krishna Srihasam wrote:
Hi,
I am analyzing my fMRI data and I got a memory alloc problem in
"mri_fwhm"
The exact message is :
mri_fwhm --mask
/tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i
/tmp/sk/FSFAST/ab
Hi,
"all.nii" takes 1309 MB. I have 4 GB RAM and a 80 GB HDD.
regards,
Krishna
Douglas N Greve wrote:
how big is all.nii and how much memory do you have on that computer?
Krishna Srihasam wrote:
Hi,
I am analyzing my fMRI data and I got a memory alloc problem in
"mri_fwhm"
The exact message
that's probably the problem then, since mri_fwhm will need about 6x the
size of all.nii. Run selxavg3-sess with the -no-fwhm option (though it
might not be in your version).
Krishna Srihasam wrote:
Hi,
"all.nii" takes 1309 MB. I have 4 GB RAM and a 80 GB HDD.
regards,
Krishna
Douglas N Greve
I would like to pose a brief question.
Somehow in the process running brains through autorecon one of my subjects
aseg.stats files became messed up and as far as I am able to tell everything
else is intact. Is there a quick way to rebuild the data that is written to
that file? Or do I have to re-r
Just run recon-all with the -segstats option, should take about 5 min or so
Kellen Mobilia wrote:
I would like to pose a brief question.
Somehow in the process running brains through autorecon one of my
subjects aseg.stats files became messed up and as far as I am able to
tell everything els
the semantics are a bit hard - it's the average mean curvature over the
parcellation unit
On Tue, 27 Jan 2009, Allison Stevens wrote:
The mean curvature for that particular parcellation.
There is a slide demonstrating curvature here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ArticlesSlidesAndP
Hi, freesurfer communityI'm Francisco Robles, from the Instituto Nacional de
Neurología y Neurocirugía in México city. I am using FS-Fast to analyze some
event-related fMRI. My problem is how to use the paradigm file because I need
to exclude some images from my analysis. The situation is that
Hi Sid,
we have the data and can replicate the bug. It's high on our priority
list.
Bruce
On Tue, 27 Jan 2009, Siddharth Srivastava wrote:
Hi Nick, Bruce,
Can you atleast suggest an alternative to get the
average volumes, that
can be used for some VBM in freesurfer. M
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