Thanks for your help, Doug.
It seems as if there is another script problem then, because when
running the command I get the following error message (log also
attached):
ERROR: Option --keep-precision unknown
I'm using Fs version 5, and the version of xhemireg I have downloaded
is: v 1.22
I could solve this problem by myself. Thanks,
(2012/05/18 14:31), Akio Yamamoto wrote:
Hi,
When I run 'make check' after successfully completing 'make' command, I
get the following message:
..
./mris_expand -v 111706 -thickness lh.white 0.5 lh.midgray
mris_expand FAILED
FAIL:
Hi,
I need to know the surface area of the structures in the aparc file
but I want to obtain this measurement from the pial surface and not
the white matter surface.
How can I do that?
Thank you a lot for your help.
ines
___
Freesurfer mailing list
Andre or Dylan (both ccd) can help
cheers
Bruce
On Fri, 18 May 2012, Zheng Hui wrote:
Hi all,
We did a scanner software upgrade to BV17 (Siemens) and lost the multi-echo
MPRAGE sequence. Does anyone have any idea where to get the sequence? The
scanner we have is a Siemens Tim Trio.
Any
Hi Akio
the test is wrong. Not sure how it happened, but we fixed this recently in
dev so you'll need to grab the new test data.
cheers
Bruce
On Fri, 18 May 2012, Akio Yamamoto wrote:
Hi,
When I run 'make check' after successfully completing 'make' command, I
get the following message:
The last argument of mris_anatomical_stats allows you to specify the
surface to use (pial in your case)
cheers,
-MH
NAME
mris_anatomical_stats
SYNOPSIS
mris_anatomical_stats [options] subjectname hemi
[surfacename]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
Hi,
Hi,
Thanks Michael.
However, when I try to do this using the aparc.annot file:
mris_anatomical_stats -l CS/label/lh.aparc.annot -b CS lh pial
I receive this error:
mris_anatomical_stats: could not scan # of lines from CS/label/lh.aparc.annot
I imagine this happens because the
You should be able to get the correct syntax by checking the recon-
all.log file for an example.
cheers,
-MH
On Fri, 2012-05-18 at 15:48 +0100, Inês Violante wrote:
Hi,
Thanks Michael.
However, when I try to do this using the aparc.annot file:
mris_anatomical_stats -l
You'll need a new version of mri_vol2vol, which I have put on that ftp site.
doug
On 05/18/2012 04:25 AM, Irene Altarelli wrote:
Thanks for your help, Doug.
It seems as if there is another script problem then, because when
running the command I get the following error message (log also
And you can get the full command line from the
$subject/scripts/recon-all.log file
doug
On 05/18/2012 10:41 AM, Michael Harms wrote:
The last argument of mris_anatomical_stats allows you to specify the
surface to use (pial in your case)
cheers,
-MH
NAME
mris_anatomical_stats
Thank you.
I've tried this command:
mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a
AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial
Would this be appropriate?
ines
On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
And you can get the full
yes, but you might want to change the name of the stats file so that you
don't overwrite the one that is there
doug
On 05/18/2012 11:39 AM, Inês Violante wrote:
Thank you.
I've tried this command:
mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a
AC/label/lh.aparc.annot -c
That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same error
that the control points are not within the mask. THis happens for all
tracts.
Thanks,
Kiely
On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
Hi Ines, this is a good thing to post to the list since there are others
that might know better than me. Also, please include the full terminal
output.
thanks
doug
On 05/18/2012 11:51 AM, Inês Violante wrote:
Thanks a lot!
Just another question:
I get this message for one of my subjects
Were the old .mat files replaced with the new ones?
On Fri, 18 May 2012, Kiely Madhavan wrote:
That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same error that
the control points are not within the mask. THis
Hi,
It repeats this several times and
MRISreadAnnotationIntoArray: vertex index out of range: 775162420
i=2E340A34, in_array_size=157940
annot file: CS/label/lh.aparc.annot
MRISreadAnnotationIntoArray: vertex index out of range: 775162420
i=2E340A34, in_array_size=157940
annot file:
I only created a diff2anat.flt.mat file which replaced the old one. Do they
all need to be recreated? If so, is that something I add to the command
line?
On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Were the old .mat files replaced with the new ones?
The other registration files depend on diff2anat. For example, diff2mni is
composed of diff2anat and anat2mni. If you're using the old diff2mni,
it's like you didn't change anything.
The -intra step creates all these. You need to edit the command that
generates the diff2anat in your version
Another note on this:
Apparently, getopt (used in fsl_sub) doesn't work correctly when this flag
is not set to 1 (it picks op a lot of options it shouldn't). Thus, instead
of commenting out the flag, it is better to set it to zero after the
set -- `getopt T:q:a:p:M:j:t:N:n:Fvm:l: $*`
Line.
What do you mean by ras matlab subscripts? Those looks like indices,
not RAS. Assuming those are indices, then that looks right.
doug
On 05/18/2012 02:02 PM, Jordan L. Poppenk wrote:
Dear Doug,
To generalize from this earlier conversion question, to interpret the
coordinate space of a file
OK - Can you point me in the direction of the trac-preproc file that I
should edit?
On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
The other registration files depend on diff2anat. For example, diff2mni is
composed of diff2anat and anat2mni. If you're
This is a script, it's in the directory where all freesurfer scripts are.
You can find it by doing which trac-preproc.
On Fri, 18 May 2012, Kiely Madhavan wrote:
OK - Can you point me in the direction of the trac-preproc file that I should
edit?
On Fri, May 18, 2012 at 12:18 PM,
That's where I looked, but all I see is the following (I don't see the
command line that creates the diff2anat for me to edit):
Last login: Fri May 18 13:45:47 on ttys000
/Applications/freesurfer/bin/trac-preproc ; exit;
Kielys-MacBook-Air:~ kielydonnelly$
This is the help text that you get when you run the script. You need to
open the script in a text editor.
On Fri, 18 May 2012, Kiely Madhavan wrote:
That's where I looked, but all I see is the following (I don't see the command
line that creates the diff2anat for me to edit):
Last login:
Hi Kiely,
In your terminal (after sourcing the freesurfer environment) type the
following:
gedit $FREESURFER_HOME/bin/trac-preproc (use pico if you're using mac, you
can also use other editors like vi or emacs)
This will open up trac-preproc script in a text editor.
you can scroll through to
Yes, use the DODS model to look for an interaction. In your case, you
will have four regressors: Group1 Intercept, G2 Intercept, G1 slope, G2
slope, so test the interaction with the contrast [0 0 1 -1]. If there is
no interaction, then run with a DOSS model and contrast [1 -1 0] to look
for a
I think this scenario applies to you (just use your structural instead
of orig.mgz).
doug
--
I have a CRS from a voxel in my functional/diffusion/ASL/rawavg/etc
mov volume and want to compute the CRS for the corresponding point in
the
Try
asegstats2table --stats=lh.roi.stats--meas volume --skip --tablefile
$OUTFILE
doug
On 05/17/2012 04:04 PM, Vy Dinh wrote:
Dear Freesurfer Experts,
I've created a couple of ROIs from qdec comparisons of thickness and
volume between two groups. We extracted the data from these ROIs for
try using mri_convert on the big file, something like
mri_convert f.nii --fsubsample 0 99 1 f.100.nii
This will extract the first 100 time points
doug
On 05/17/2012 04:48 PM, Guthormsen, Amy M wrote:
Hello,
I would like to use fsfast to analyze retinotopic data that I
collected. I used the
Hi Aaron, probably the easiest thing to do is to re-run mri_segstats for
each of your subjects giving it the option to save this measure into the
output stats file. To do this, you can get the basic command from the
recon-all.log file. To this add
--brainmask mri/brainmask.mgz
ps. This will automatically be done in the next version, and you should
be able to find this info in the wmparc.stats file already.
On 05/17/2012 04:56 PM, Goldman, Aaron (NIH/NIMH) [C] wrote:
Hello,
For an analysis, we’re trying to calculate a Total Brain Volume
covariate based on the
Hi Bruce
I have confirmed that all tests are passed.
Thanks,
Akio
(2012/05/18 23:37), Bruce Fischl wrote:
Hi Akio
the test is wrong. Not sure how it happened, but we fixed this
recently in dev so you'll need to grab the new test data.
cheers
Bruce
On Fri, 18 May 2012, Akio Yamamoto
How did I miss this asegstats2table script? It looks great...and here I've
been writing my own bash scripts to get the data out.
-
J
On Fri, May 18, 2012 at 1:59 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Try
asegstats2table --stats=lh.roi.stats--meas volume --skip --tablefile
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