Dear Tracula Team,
recently i ran trac-all (-prep / -bedp / -path), but I happened to submit the
commands to our SGE computer cluster using fsl_sub (which is fsl's wrapper for
qsub)
According to the header comments of the trac-all script, however, trac-all
should not be submitted to a
Dear freesurfer users,
I have tried to run generate stats data tables, but I have that error message:
asegstats2table --common-segs --meas volume --tablefile
/home/charlotte/TROISCITES/DATA/FREESURFER/qdec/stats_tables/aseg.volume.stats.dat
--statsfile=aseg.stats --subjects 10049 10053 10079
Hello,
Anyone have a chance to look at this? Should we just forget about
trying to get an accurate lhCorticalWhiteMatterVol value for this
subject?
thanks,
-MH
On Tue, 2012-02-21 at 15:35 -0600, Michael Harms wrote:
Hi guys,
We have a subject processed with FS v5.1 in which
oh, sorry, I do remember now that we took that out (I think we put it
back in for the next release). The work-around is to run
mri_binarize --i brain.mgz --min 0.1 --count count.dat --o junk.mgh
You can delete junk.mgh. The file count.dat will have info about the
number of voxels in the
Hi Mike, can you upload the subject and I'll take a look?
doug
Michael Harms wrote:
Hello,
Anyone have a chance to look at this? Should we just forget about
trying to get an accurate lhCorticalWhiteMatterVol value for this
subject?
thanks,
-MH
On Tue, 2012-02-21 at 15:35 -0600,
Have you looked at that file to see if there is anything in it?
Sometimes the file gets created but not filled with any information
(maybe the disk is full).
doug
Charlotte Bernard wrote:
Dear freesurfer users,
I have tried to run generate stats data tables, but I have that
error message:
You'll have to run it on each subject. Easy to do with a script. You can
then cat the data into one fine (they are just text files).
doug
Rashmi Singh wrote:
Thanks Doug,
Do I need to run the following for each subject or can is there a way to
run it with input for all my subjects in one go
Hi Andi - Thanks for your kind words!
As explained on the trac-all wiki page (and also the help text you get
from trac-all --help), the part about not submitting trac-all with
pbsubmit is specific to our local Martinos Center users.
That's b/c we've modified fsl_sub (and bedpostx) to work
Dear all,
Given a series of fsaverage-registered rCBF maps, I am trying to extract
the average rCBF value from one specific region. This region, which was a
significant cluster from a volumetric (fsl) analysis, was binarized and
then converted to surface.
When I run mri_segstats with the --avgwf
Hi Doug,
Below is the output in the terminal window from running the analysis to the
crash. Attached are the qdec.fsgd and y.fsgd files from the qdec output.
I'm not actually sure what these file represent - could you enlighten me?
Thanks!
Laura.
Number of subjects: 55
Number of factors:
Hi Doug,
I created a new first level analysis along with new contrasts and event
numbers for a group of subjects I had previously done analyses on. All but
one of the subjects finished selxavg3 without error, but one subject gave
the following error:
Saving X matrix to
Hi All,
Is there a way to calculate the length and width of a label ?
Please let me know.
Thanks a lot
Ri
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The information in
sorry, I don't think so
On Wed, 29 Feb 2012, Ritobrato Datta wrote:
Hi All,
Is there a way to calculate the length and width of a label ?
Please let me know.
Thanks a lot
Ri
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Hi Marco,
The columns correspond to the integer IDs in the --seg image, so assuming
you passed in a binary mask the first column is mean over everything that
isn't your ROI and the second column is the mean in your ROI.
Cheers,
Michael
On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia
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