if this refers to a previous email, then make sure to include previous
correspondence. in any event, I don't know what you did and can't help
you until I find out
On 12/14/2015 06:11 PM, Arnaud Boré wrote:
> Dear Freesurfer's experts,
>
> I wanted to add this picture so you can understand better
Hi,
I’m running freesurfer 6 on a cluster. I am having issues with the matlab
crashing during the hippocampal segmentation. I am allocating 10gb for each
job, however that hasn’t fixed the problem. Sometime the segmentation works
fine, however many segmentations fail due to matlab crash. I hav
Dear experts,
I've been attempting to generate a stats data table in qdec, but each time
I get a "Index Error: list index is out of range" error. This is occurring
when it is trying to parse the .stats file.
I've made sure that the files all line up exactly with the qdec table and
that SUBJECTS_
Dear Freesurfer users, (apologies for cross-post)
I am pleased to announce the release of an R package I created, called
"brainGraph", for performing graph theory analyses of brain MRI data. You can
use it for cortical thickness, volume, surface area, or LGI. It can also be
used for tractograph
Hi Virenda
can you say what you mean by 20% errors? Compared to what? Note for
example that a 20% variation in the thickness at one spot would mean a
change of 0.4mm (for 2mm thick cortex). Seeing this type of variation
point-wise somewhere in the brain isn't terribly surprising, although I
w
Hi Elisabetta
can you describe what you did in this case? I'm puzzled because the
brain.finalsurfs.mgz and the wm.mgz both contain skull in them and don't
like they have been skull stripped at all, but the brainmask.auto.mgz
(which is the output of our skull stripping) looks like it worked well
Hi,
I will appreciate if somebody could reply to my message that was posted
earlier. I copy-paste the message here again.
We are currently in the process of analyzing some data that was defaced using
mri_deface command of freesurfer. This defaced data was then used as an input
to recon-all and
Did you source the Freesurfer setup script?
$> export FREESURFER_HOME=/Applications/freesurfer6
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh
> Hello All,
>
> I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am
> getting the following error when I run recon-all from free
you can use mris_apply_reg to apply the resulting registration (may need
to get you a copy)
On 12/14/2015 08:24 AM, Bruce Fischl wrote:
> Hi Christopher
>
> mris_left_righ_register will do the trick, although Doug might have
> something else. Give it the left and right sphere files as input and
Try mris_left_right_register
On 12/14/2015 02:42 AM, Milde, Christopher wrote:
>
> Dear Freesurfer experts,
> is there a way to perform an interhemispheric registration with rh, lh
> surfaces in native space?
> Preferentially, I would perform the registration with smoothwm surfaces.
> I only foun
Hi,
I am trying to convert MNI coordinates to a subject's anatomical space
surf coordinates.
While this
MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'
works fine from surf coordinates to MNI I don't know how to make it
work correctly the other way around...
i.e., knowing MNI305RAS and w
Dear All,
Are these two .gca files applicable to macaque brain processing?
1- RB_all_2008-03-26.gca
2- RB_all_withskull_2008-03-26.gca
if not, is there any procedure to make these two files for non-human
primates ?
I really appreciate any help or insight.
Thank you,
Mahmoud
if it's only on one subject then it probably isn't an orientation
problem. Checking it just means bringing it up in freeview and making
sure that the directions that freeview shows (left/right, I/S, A/P) are
actually the anatomical ones in the image.
Probably the orientation is right and the ta
Hi Christopher
mris_left_righ_register will do the trick, although Doug might have
something else. Give it the left and right sphere files as input and
specify the registered left and right spheres as output
cheers
Bruce
On Mon, 14 Dec 2015, Milde, Christopher wrote:
Dear Freesurfer
Hi Richard,
This occurs because the gaps exist in the original fsaverage5
split_component parcellation. As explained in the documentation text
file (Yeo_JNeurophysiol11_SplitLabels_README which should also be
included in the zip file), one of the steps taken to generate
*.split_components.annot in
Hi Bruce,
How can I check if I have the correct orientation ? The initial image look
as classical T1 weighted.
I have the problem only on one subject above all, so that sounds like an
exception ?
Best regards,
Matthieu
2015-12-11 14:49 GMT+01:00 Bruce Fischl :
> did it have the correct orient
Hi Prof,
Thanks for the speedy reply,
When you specify fsaverage5 as -srcsubject and your own subject as -trgsubject,
the code executes but the resulting .annot file looks like a mess.
Your proposed two-step call to mri_surf2surf seems more promising. If I run the
following:
mri_surf2sur
Hi Freesurfer experts!
I tried to run recon-all base for a longitudinal analysis on my data. But I get
the following error:
Excessive topologic defect encountered: could not allocate 221309241 edges for
retessellation
Cannot allocate memory
Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #
18 matches
Mail list logo
