Gesendet: Sonntag, 23. August 2015 um 17:06 Uhr
Von: "car...@van-vlodrop.de"
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Did not find any volume geometry information in the surface
Dear Freesurfer experts,
I have run a Monte Carlo simulation and uploaded the results in freeview with th
Hello FS experts and all,I would like to find out the magnitude of the group
difference between a two-group comparison (e.g. percent difference on cortical
thickness indicating how much one group differs from the other.) I have run
analysis using both mri_glmfit and qdec, I also run cluster wise
Dear Freesurfer experts,
It seems impossible to load ?h.aparc.annot annotation file on ?h.pial
surface of the fsaverage_sym subject. When I try under freeview, it crashes
and gives me this error :
*Did not find any volume geometry information in the surfacepBDid not fin
Dear Freesurfer experts
I have run an ROI analysis in Freesurfer using two different strategies
and I would have expected the results to be the same (or similar), but
they are not and I don't really understand why.
I have an ROI that I obtained from an atlas in MNI space and projected
to the
Dear Experts,
With your help, I recalculated the surface area, now using the pial surface
instead of the wm/gm boundary. I am, however, somewhat surprised by the
discrepancy between my previous and current results, because the cortical
surface area that is calculated using the pial is surface i
Niels,
Why do you expect the surface area to be the same between the two different
surfaces pial, and white?
hth
d
On Fri, Aug 28, 2015 at 8:23 AM, Gerrits, Niels wrote:
> Dear Experts,
>
> With your help, I recalculated the surface area, now using the pial
> surface instead of the wm/gm boun
Dear Experts,
I still got a super big cluster that covers the whole brain for the F test,
please help...
Thanks,
Lena
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: 21 August 2015 19:07
To: freesurfer@nmr.mgh.har
Hi Niels
why are you surprised that the pial surface has significantly more
surface area than the white? It would seem like it must.
Bruce
On Fri, 28 Aug 2015, Gerrits, Niels wrote:
Dear Experts,
With your help, I recalculated the surface area, now using the pial surface
instead of the wm
it looks like you have the correct design. I would look for an
interaction between group and age (contrast 0 0 1 -1) in the dods model.
If there is none, then go to a doss model with 1 -1 0 contrast. If there
is an interaction, then some say you cannot test for a simple difference
in the groups
On 8/27/15 1:13 PM, Francesco Puccettone wrote:
Hello all,
I have seen several (older) papers that draw conclusions about the
implication of a brain region in a given task by using the following
logic: region X was activated in the contrast /taskA>baseline/, but
not in the contrast /taskB>b
On 8/27/15 1:20 PM, Francesco Puccettone wrote:
Sorry, forgot to add one additional (related) question:
is it ever correct to say "for region Y, the activations found for
taskA were smaller than for taskB" just based on the two contrasts
/taskA>baseline /and /taskB>baseline/? Or is it necess
You can ignore that warning. It has been fixed in the next version.
On 8/28/15 3:25 AM, car...@van-vlodrop.de wrote:
*Gesendet:* Sonntag, 23. August 2015 um 17:06 Uhr
*Von:* "car...@van-vlodrop.de"
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Did not find any volume geometry information in t
There are a couple of things you can do.
You can create a contrast for each group separately, then compute the
voxel-wise percent difference between the maps, eg,
fscalc group1/gamma.mgh pctdiff group2/gamma.mgh -o pctdiff.mgh
You can compute the percent differences from the average in the
what is your command line? Can you run it without the annotation?
On 8/28/15 5:58 AM, Matthieu Vanhoutte wrote:
Dear Freesurfer experts,
It seems impossible to load ?h.aparc.annot annotation file on ?h.pial
surface of the fsaverage_sym subject. When I try under freeview, it
crashes and gives
did you use the new contrast?
On 8/28/15 9:49 AM, Lim, Lena wrote:
Dear Experts,
I still got a super big cluster that covers the whole brain for the F
test, please help…
Thanks,
Lena
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf
1) Why is there a difference between the 2 methods for area but not
thickness ?
Area needs a jacobian correction and thickness does not
2) What is the 'correct' method for area (if any) ? Or is there a better
method for an ROI analysis of area?
If you are going to use mri_surf2surf, then add
No, QDEC is a very limited tool. You'll have to use the command line
(mri_glmfit-sim). Also, you'll need to register each of your subjects to
the new atlas (surfreg), then specify the average subject AND the new
registration when running mris_preproc to create a new y.mgh file. None
of this can
it might be. Try lowering the threshold to see if the other clusters appear
On 8/27/15 10:32 AM, Kai Jannusch wrote:
Dear all,
After my analysis for pial_lgi using fsaverage as common space
subject, I started a Monte Carlo correction in Qdec.
The terminal lists the significant clusters afte
I launched freeview, then added manually lh.pial and rh.pial of
fsaverage_sym. A this point all is OK.
Then it crashed when I try to load graphically lh.aparc.annot or
rh.aparc.annot. I viewed that in freesurfer mailing, this problem has been
told in the beginning of 2014 but nothing afterthen.
D
You will have to rerun the analysis using mri_glmfit-sim. This will
create a text file with a list of values for each subject. Run
mri_glmfit-sim with --help to get more info
On 8/26/15 11:55 AM, pablo najt wrote:
Dear FS experts,
Reposting my message below.
Thanks
I have run two group compa
Hi Doug -
I've been experimenting with different approaches to link freesurfer
with matlab but to no avail. Any assistance would be greatly
appreciated.
The most recent attempt used the following code.
In a fresh terminal window (tsch) I'd set the environment for
FREESURFER_HOME and SUBJECTS_DI
Hi Matthieu
I believe you can use
freeview -f lh.inflated:annot=lh.aparc.annot
check out freeview -help. It lists this type of option
cheers
Bruce
On Fri, 28 Aug 2015, Matthieu
Vanhoutte wrote:
> I launched freeview, then added manually lh.pial and rh.pial of
> fsaverage_sym. A this point al
what slice order was the data created with? Find out and then use that
slice order in the command
On 8/26/15 4:14 AM, std...@virgilio.it wrote:
Hi list,
I'm performing slice time correction on preproc-sess -s Sess201 -fwhm
5 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run.
I have acqui
Would it be possible to send us lh.pial and lh.aparc.annot that caused the
crash?
Best,
Ruopeng
On Aug 28, 2015, at 10:59 AM, Matthieu Vanhoutte
wrote:
> I launched freeview, then added manually lh.pial and rh.pial of
> fsaverage_sym. A this point all is OK.
>
> Then it crashed when I try t
Hello Bruce,
I try your command but freeview crashed with this message error :
freeview -f surf/lh.inflated:annot=label/lh.aparc.annot
*Did not find any volume geometry information in the surfacepBreading
colortable from annotation file...colortable with 1036 entries rea
I can do it. Where could I send you these files ?
Best regards,
Matthieu
2015-08-28 17:12 GMT+02:00 Ruopeng Wang :
> Would it be possible to send us lh.pial and lh.aparc.annot that caused the
> crash?
>
> Best,
> Ruopeng
>
> On Aug 28, 2015, at 10:59 AM, Matthieu Vanhoutte <
> matthieuvanhou...
If the files are not big, you can just email them to me. Otherwise you can use
file drop:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks,
Ruopeng
On Aug 28, 2015, at 11:23 AM, Matthieu Vanhoutte
wrote:
> I can do it. Where could I send you these files ?
>
> Best regards,
>
> Matthieu
>
Thanks for sending me the files. I have no issue loading the annotation file
using the latest freeview build. I assume you are still running an old version
that comes with freesurfer 5.3 official release. You can download the latest
freeview dev build here and give it a try:
https://surfer.nmr.
Not sure what is going on. Try creating a symlink to matlab from a
location in your path, eg, if ~/bin is in your path, then
cd ~/bin
ln -s /Applications/MATLAB_R2014b.app/bin/matlab matlab
rehash
then run again
On 8/28/15 11:04 AM, Gay,Charles Wysaw wrote:
> Hi Doug -
> I've been experimenting
After taking a look through some of these subjects, it appears there is low
contrast between white and gray matter. The gray matter has higher intensity
than what is normally expected by Freesurfer. Re-running the subjects with
expert options that raise the lower intensity threshold for whit
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