Hi again Christophe,
Yes thank you, this does makes things much more clear.
I still have a few questions:
1) I would like to confirm that the '?h.aparc.a2005s.annot' parcellization
refers to the labels generated by the 2002, 2005, and 2009 atlases (and
that one can output their results to table
Hi Nick,
> during the skull strip stage, an alignment to an atlas is computed,
> which takes quite a bit of time (40-60 minutes).
Just so you know, this isn't included in the approximate timings in
the help for recon-all, which seem to suggest that autorecon1 should
be more like 15 minutes in tot
Dear FreeSurfers,
I wanted just eTIV from a bunch of subjects, and it looked to me from
an example log file that both old (with skull) and new (without)
estimates would be available after autorecon1, since registration with
and without skull seems to have been performed early on. However, I've
not
I would be interested in this as well.
-Derin
On Oct 16, 2009, at 11:40 AM, Doug Greve wrote:
>
> Good point (meaning that I don't know the answer). I'll see if I can
> find out.
>
> doug
>
>
>
> On Fri, 16 Oct 2009, Donna Dierker wrote:
>
>> Regardless: FDR's sensitivity appears resolution-de
you might try mris_volmask. It expects two surfaces (usually "white" and
"pial"),
so you might have to generate a 2nd surface with mri_surf2surf with
--surf-xyz, --targ-xyz, and --projabs XXX (XXX =? 1mm).
doug
On Fri, 16 Oct 2009, Daniel G. Wakeman wrote:
> Hi,
>
> I need to generate a mask
Hi,
I need to generate a mask from a 'BEM' surface (10242 vertices). I
have tried doing this utililzing mri_surf2vol; however, this doesn't
produce a good mask as only the vertices are utilized creating a
speckled volume. Is there any way to create a proper mask utilizing
all of the surfac
Good point (meaning that I don't know the answer). I'll see if I can
find out.
doug
On Fri, 16 Oct 2009, Donna Dierker wrote:
> Regardless: FDR's sensitivity appears resolution-dependent to me.
>
> On 10/16/2009 10:39 AM, Michael Harms wrote:
>> Interesting post Donna, but my understanding o
Regardless: FDR's sensitivity appears resolution-dependent to me.
On 10/16/2009 10:39 AM, Michael Harms wrote:
> Interesting post Donna, but my understanding of FDR is that it sets the
> p-value threshold based on the LARGEST p-value that satisfies the FDR
> relationship.
>
> That is, steps 3 and
mri_nu_correct is just a wrapper script created by us for nu_correct.
the wrapper script just does some extra file conversions (mgz to/from
mnc).
nick
On Fri, 2009-10-16 at 12:19 +0100, McLean John (NHS Greater Glasgow &
Clyde) wrote:
> > Hi,
> >
> > What's the difference between applying nu_corr
a memory leak in mris_volmask was fixed in v4.5. this leak is very
likely the source of the segfault you are seeing. either upgrade to
v4.5, or you can get a fixed mris_volmask.bin here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc
copy it to your $FREESURFER_HOME/bin dir.
nick
when testing (retesting) the -autorecon1 stage, be sure to include the
-clean-lta (or -clean) flag. during the skull strip stage, an alignment
to an atlas is computed, which takes quite a bit of time (40-60
minutes). if -autorecon1 is rerun, and the .lta file produced by a
prior run is detected,
Interesting post Donna, but my understanding of FDR is that it sets the
p-value threshold based on the LARGEST p-value that satisfies the FDR
relationship.
That is, steps 3 and 4 in Genovese et al. (2002) are:
3) Let r be the largest i for which p <= i/V*q (assuming c=1)
4) Threshold the image a
I never heard anything on my post here, but it might just be high
surface resolution:
http://www.mail-archive.com/neuro-mult-c...@brainvis.wustl.edu/msg00026.html
On 10/16/2009 09:58 AM, Michael Harms wrote:
> Your FDR analysis sounds correct. You probably have a rather small
> number of "margi
Your FDR analysis sounds correct. You probably have a rather small
number of "marginally" significant vertices, which is why none survive
FDR. You could try increasing the "q" value from say 0.05 to 0.1, in
which case 10% of the surviving vertices would be expected to be false
positives.
cheers
autorecon2 takes about 15.5 hours on the Blade 2.0 GHz running FS v4.5 versus
9.8 hours on the 3.2 GHz computer running v4.0.5, but this is in line with the
increased clock speed of the second computer (1.6x faster than the Blade).
Thanks, Chris
>>> Bruce Fischl 10/16/09 7:25 AM >>>
are all th
Hi,Marie
In the paper "A surface based approach to quantify local gyrification" on TMI.
There is a discussion the relation between lGI and curvature-based method. I
noticed the following discussion:
"In the current study, all the GI measurements were computed on cortical
surfaces based on ima
are all the steps taking longer, or are some binaries longer than others
On Thu, 15 Oct 2009, Alexander Zaitsev
(CNI) wrote:
> We are having the same issue after upgrade to FreeSurfer 4.5.
> It takes more than 1.5 hrs for the jobs that used to complete in less
> than 30 minutes.
>
> Alex Zaitse
> Hi,
>
> What's the difference between applying nu_correct and mri_nu_correct?
>
> Many thanks
> John
This message may contain confidential information. If you are not the intende
Hi Chrisophe,
Thanks very much for your answer but I'm not sure I understand. I see the
below labels in the '?h.aparc.a2005s.annot' label files generated by
freesurfer version 4.4 as well as in those generated by freesurfer version
3.0.5:
'S_temporal_transverse'
'G_temp_sup-G_temp_transv_and_in
Dear experts,
The recon-all process of some of my subjects (15 from 100) exited with
ERRORS ...
I got in the recon-all file of one of them the following report:
...
Reporting on 49 segmentations
#
#...@# Cortical ribbon mask Sat Aug 29 13:09:43 CEST
Dear Freesurfer team,
We are currently doing a cortical thickness studies between a group of
psychiatric patients (n=60) and controls (n=30). We tested several
smoothing levels (15mm, 20mm, 25mm)
When setting an uncorrected threshold (such as p<0.005), we obtained
several regions of decreas
Dear Freesurfers,
I have 2 identical DTI sequences for each patient (adquired within the same
session), but would like to work with the average DTI sequence in all my
subsequent analysis. How to obtain the average of both DTI sequences with
Freesurfer, and convert the resulting file into .nii?
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