Dear FS experts
I am using high resolution (0.75x0.75x0.75 mm) data within FS but the
following error occurred:
...
vertex spacing 0.69 +- 0.21 (0.00-->6.06) (max @ vno 265258 --> 114262)
face area 0.19 +- 0.10 (0.00-->4.49)
mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (err
Perhaps I should have asked:
Do I need to separately install FSL?
Thanks
> Hi,
>
> I ran the following preproc-sess command and mkbrainmask-sess failed, with
> an error message of not finding fsmaths. I don't know where to be looking
> for this file and what previous command should have generated
Hello. I just installed FreeSurfer v4.4.0, following all the directions to
the letter. When I run recon-all -i -s -autorecon1,
I get the following error:
Can't locate MNI/Startup.pm in @INC (@INC contains:
/System/Library/Perl/5.8.6/darwin-thread-multi-2level
/System/Library/Perl/5.8.6 /Librar
Hi Jared,
yes, the talairach.m3z is the intersubject registration we use for
generating the aseg, and you could use it to compute a dice.
cheers
Bruce
On Tue, 30 Jun 2009, Jared Price wrote:
Hi freesurfer masters,
Quick question on the way freesurfer calculates the dice coefficient. I am
Hi,
I ran the following preproc-sess command and mkbrainmask-sess failed, with
an error message of not finding fsmaths. I don't know where to be looking
for this file and what previous command should have generated it. Can
anyone help me out?
Thanks!
Dahlia.
I ran:
preproc-sess -sf sessid_subj31
Hi freesurfer masters,
Quick question on the way freesurfer calculates the dice coefficient. I
am interested in getting an INTERsubject dice coefficient as a measure
of similarity between 2 subjects. My question is, do I need to do an
INTERsubject registration step before calculating the dice
Hi Avi,
do you have any advise for Dana?
thanks
Bruce
On Tue, 30 Jun 2009, Dana W. Moore wrote:
Doug
Yes, there is an error message in the talairach_avi.log--I am not sure what
it means. The end of the log gives me this message:
Dana
imgrege: no voxels in register
ERROR: 'imgreg_4dfp /u
Doug
Yes, there is an error message in the talairach_avi.log--I am not
sure what it means. The end of the log gives me this message:
Dana
imgrege: no voxels in register
ERROR: 'imgreg_4dfp
/usr/local/freesurfer/average/711-2C_as_mni_average_305
/usr/local/freesurfer/average/711-2B_as_mni_av
Hi Jidan,
The surface in the native space is given by ?h.white.
?h.sphere and ?h.sphere.reg provide the "mapping" of those vertices of
to a spherical representation, and registered spherical representation,
respectively. There are ways to get at the Jacobian of these
transformations if that is w
Hi Fatima,
can you send us the recon-all.log?
thanks
Bruce
On Tue, 30 Jun 2009, Ahmed, F, Me
wrote:
Hi,
I had problems running autorecon 1 with my own subject group, so I decided to
see if I could run the tutorial with Bert. I ran the motion correction, and
then tried autorecon 1 and got
Hi Feng-Xian,
the surfaces all live in the surf subdirectory. To see how many vertices a
surface contains you can run either mris_euler_numer of mris_info. The
thickness is in the ?h.thickness ("curv" format file - one scalar per
vertex) and the inflated is in ?h.inflated surface format. You c
how much ram do you have on your machine?
On Tue, 30 Jun 2009
whb...@mail.ustc.edu.cn wrote:
Hello!
I just setup "freesurfer-Linux-centos4-stable-pub-v4.4.0" on linux
2.6.21-1.3194.fc7 . to test freesurfer, I successfully run "recon-all -s bert
-autorecon1" and "recon-all -s bert -autorecon3
Hi,
I had problems running autorecon 1 with my own subject group, so I decided to
see if I could run the tutorial with Bert. I ran the motion correction, and
then tried autorecon 1 and got the following error (please see the attached
word document to see my output).
ERROR: converting nu to COR
Hi,
I want to check the image matrix after doing autorecon-all. When I look
at the text, I see that “Original Data has (1, 1, 1) mm size and (224, 256,
160) voxels. Data is conformed to 1 mm size and 256 voxels for all
directions”. This is said that that image matrix is 256 x 256 x 256. Righ
Hello!
I just setup "freesurfer-Linux-centos4-stable-pub-v4.4.0" on linux
2.6.21-1.3194.fc7 . to test freesurfer, I successfully run "recon-all -s bert
-autorecon1" and "recon-all -s bert -autorecon3", but "recon-all -s bert
-autorecon2", exited with ERRORS,as follows:
"writing output transfor
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