Dear All,
I have some basic questions about groups analysis for cortical thickness, and I
looked over the list and tutorial, but still have questions.
I have two groups, experimental and control, and both were tested before and
after training...
I plan to use qdec to run the group analysis, and
Hi Jon - You can try merging the DWIs, gradient tables, and b-value files
from the 2 scans and specifying the merged version in the config file as
if this were a single scan. I haven't tried this myself, so do let me know
if this works!
If in addition to 2 DWIs you also had 2 anatomicals, you
Hi Bruce
Thank you for your answer...
My concern is that the left pial surface of the medial orbitofrontal cortex is
overlapping the right medial orbitofrontal cortex... I don't think that the
cortical thickness can be accurate if so...?
Thank you very much in advance for your help...
Best regard
Hi Andi - You're very welcome! I hope you'll find it useful.
That's correct, if you turn off these pre-processing options then trac-all
will simply copy your DWIs, gradient table and b-value table from the
location that you specify to the dmri/ directory and continue from there.
You can cert
Why do you think left and right are mixed up? The image looks fine. What does
the aseg look like?
Cheers
Bruce
On Mar 4, 2013, at 1:01 PM, aurore curie wrote:
> Hi
> I have a problem with one of the brain I am analysing...
> It seems like Freesurfer mixed the right and left hemisphere (see t
*[posting for colleagues, please write to them, not to me]
*
*
*
Research Assistant Position in Cognitive Neuroscience
Department of Neurology, School of Medicine, New York University
We are seeking a full-time Research Assistant to assist with cognitive
neuroscience experiments involving human
Hi Nick,
Congratulations and thank you and the whole team (the Freesurfites)
very much for your efforts.
Cheers,
Ed
On 03 Mar, 2013, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>
> Freesurfers,
>
> At long last, a new version of Freesurfer is available for download!
>
> For a list o
hello,
we have acquired dti scans on a subject during a FMRI experiment. is it
possible to process both dti's with tracule to get an average of the 2 dti's?
If so, how do I setup the config file for this?
Thanks
Jon
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Sinead,
Much has improved since v4.5, so I would recommend updating to v5.2. I
would have to re-run your prior subject data, as you will not be able to
mix results processed with different versions, but any edits you made will
be retained.
The mris_volmask failure you describe will not invalidat
Hi Nick,
Thanks for your help. I'm running v4.5.0 on our cluster. I'm don't think
the latest version has been installed. I might just ask them to install
v5.2. Should I re-run the recon_all steps again with this latest version?
Should I disregard the results that have already been computed with th
Isabelle,
If gcut fails, and you've exhausted the various threshold options (per the
tutorial on brainmask fixes), then i think the only option is to manually
edit the brainmask.
Nick
> Good morning,
>
> I tried to run the following command:
>
> recon-all -skullstrip -clean-bm -gcut -subjid S01
Chikku,
remove FILE from the command line, it should just be:
--tablefile aseg.vol.table
Nick
> Dear all,
> I am getting and error when trying this command,
> asegstats2table -s truetest1 truetest2 \ --segno 11 12 17 18 \
> --tablefile FILE aseg.vol.table
> ERROR: output table name should b
Sinead
Are you running v5.0.0? This link has some info on fixing the problem,
something your admin will have to do:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012846.html
Or better yet you can them install install v5.2, which doesnt have that
dependency in mris_volmask
Dear FS experts,
I have multiple anatomical scans acquired on a 3T Philips scanner. The image
quality is not the greatest and when I used recon-all –autorecon1 to remove the
skull, I noticed that for many scans, the algorithm was not able to find the
boundary between the brain and the skull. I
Hi Andreas,
no, I don't think we ever generated one. I guess we could if people found
it useful, or you could do it and contribute yours.
cheers
Bruce
On Mon, 4 Mar 2013,
Andreas Werner wrote:
Dear Freesurfer list,
I was wondering, whether a standard flatmap of the occipital lobe in fsaver
Good morning,
I tried to run the following command:
recon-all -skullstrip -clean-bm -gcut -subjid S01
to remove the skull and remaining dura mater. However, for some subjects, I
get the following error:
** Gcutted brain is much smaller than the mask!
** Using the mask as the output instead!
Dear all,
I am getting and error when trying this command,
asegstats2table -s truetest1 truetest2 \ --segno 11 12 17 18 \
--tablefile FILE aseg.vol.table
ERROR: output table name should be specified (use --tablefile FILE)
child process exited abnormally command.I tried using
Any Help
Chikku
Dear members,
I am currently conducting cortical thickness analysis and I have ran the
recon_all step. The appropriate files have been created including aseg.mgz,
brainmask.mgz, aseg.stats etc. and therefore volumes and cortical thickness
measures have been calculated, however, when I look at the
Dear Tracula Team,
first, thank you very much for the new version with its many improvements !
I have dwi data (as nii.gz) that have already been unwarped and eddy-corrected,
the bvector-textfiles have also been rotated accordingly.
So, I guess, when I use TRACULA on these data, I simply set dob
Thank you Doug!
This is a great suggestion and will prevent me from getting lost in the
different analyses. And it will also offer the opportunity to analyze
subjects from the two different cohorts together without coping the data
in one SUBJECTS_DIR.
Thanks again!
Best regards, Katharina
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