On 08/15/2014 10:33 PM, Chung, Yoonho wrote:
> Hi,
>
> I am running Hippocampal subfield processing stream and I think I got all the
> appropriate "posterior_*.mgz files" I need to get the stats, but I am not
> seeing "nonPartialVolumeStatsRight.txt" anywhere as described in the wiki
> under $
Hello FreeSurfers,
during the course of my diploma thesis i wrote a few R functions around
FreeSurfer, mainly for group analysis of FreeSurfer surface data in R. I
thought i'd just contribute the code here, on the off chance that
someone may find it useful, and despite the code quality (i wrote th
Hi FreeSurfers,
i came across a few subjects in which FreeSurfer 5.3 failed to properly label
most of the hippocampus in one hemisphere. Specifically, it is the left
hippocampus in all of the 5 cases in which this occured. The subjects are
young, healthy, and without any anatomical peculiaritie
June 05, 2013 23:22:46 Douglas N Greve wrote:
> Hi Andreas, it is not the same method but somewhat related. The method
> assures that total area (or volume) is preserved when mapping between
> subjects. How much detail do you need?
> doug
>
> On 06/04/2013 05:21 AM, An
Hello FreeSurfers,
after reading this [1] paper about measuring surface area, i realized i don't
know what the default way of measuring surface area is in FreeSurfer. Is it
similar to what's described in the paper? Could you point me to the right
documentation or publication?
Forgive me if i've
Hi surfers,
as of FreeSurfer version 5.3, i am missing the option to choose between DOSS
and DODS design in QDEC. The radiobuttons in the design tab are no longer
there. The default behaviour, judging from the results, seems to be DODS. Has
this option been removed?
regards,
Andreas
_
> On 04/24/2013 09:51 AM, Andreas Berger wrote:
> > Hi Surfers,
> >
> > as of version 5.2, i'm getting an error using asegstats2table, depending
> > on how i sort the subjects:
> >
> >
> > andreas@psy058:~$ asegstats2table --subjects $(ls $SUBJECT
Hi Surfers,
as of version 5.2, i'm getting an error using asegstats2table, depending on
how i sort the subjects:
andreas@psy058:~$ asegstats2table --subjects $(ls $SUBJECTS_DIR | sort -t _ -k
1 -nk 2) -t segstats.csv --skip -d comma
SUBJECTS_DIR : /mnt/raid/freesurfer/subjects
Parsing the .sta
On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote:
> Hi Doug
>
> Strangely, the basic mri_concat command now worked, and so did the full
> one. I think I initially had a "\" at the end of my command, just after the
> file name, which should not have been there; although having tried again
On Monday, December 03, 2012 13:46:11 charles laidi wrote:
> Dear freesurfers.
>
> I'm using freesurfer for two weeks. I'm currently trying to make a script
> to get asegstats resultats for >100 patients.
>
> I did this script in tcsh :
>
> foreach filename (t1_)
> asegstats2table --subj
On Sunday, December 02, 2012 23:56:38 Yaniv Kaufman wrote:
> Dear Freesurfer experts,
>
> I am trying to display DTI using freeview, however, every time I attempt to
> run freeview from the command line (I am using Ubuntu 12.4), I receive the
> following error:
>
> "freeview.bin: error whil
hi,
that line from the wiki appears to be in tcsh syntax, you are using bash,
which is the default shell of most operating systems. you can try either in
bash, like this:
if [ ! -e fsaverage ]; then ln -s $FREESURFER_HOME/subjects/fsaverage; fi
...or in tcsh, which you might need to install fi
take a look?
> Allison
>
> --
>
> On Mon, 22 Nov 2010, Andreas Berger wrote:
>
> > Hello Surfers,
> >
> > we just finished processing our subjects (recon-all -all) with freesurfer
> > version 5.0. In 16 out of 240 subjects i found severe errors: in about 4
reenshots?
>
> --
>
> On Tue, 13 Apr 2010, Andreas Berger wrote:
>
> > on one group of subjects i ran "recon-all -all -clean -wsthresh n", which
> > according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
> > includes what "-c
hresh, change the skull strip
> for the better?
>
> when you ran it on the already clean data set, you said using -wsthresh 0
> still did not get a good skull strip?
> Allison
>
> --
>
> On Fri, 9 Apr 2010, Andreas Berger wrote:
>
> > Sorry for the sl
running? The 32 and 64 bit versions will definitely
> have differences - it's unavoidable. In the newest version we did eliminate
> some of the randomness that reduced reproducibility though.
>
> Bruce
>
> On Sat, 13 Feb 2010, Andreas Berger
> wrote:
>
> > H
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