Dear FreeSurfer Experts,
I have a data set (control and patients) that has 3D MPRAGE (no visual
brain pathologies in both groups), acquired on 1.5 T Siemens scanner after post
contract (Gadolinium). Can I use his data set to measure the cortical
thickness? Is gadolinium can interferes the cortica
Dear FreeSurfer experts,
we are using FLAIR images to improve pial surface detection. In many cases this
works OK, however, in some cases this procedure fails and the corrected pial
surfaces are much worse than before.
I uploaded 2 example subjects FLAIRpial_OK and FLAIRpial_not_OK to
ftp://s
Dear FreeSurfer experts,
could you please look at the issue mentioned below? I did not receive any
answer to my post, probably it got lost unattended.
Antonin Skoch
_
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
To: Antonin Skoch [mailto:a...@medicon.cz]
Cc: Nick Schmansky [ma
*Dear Freesurfer experts,
**I have encountered the following error while running the tracula
**pre-processing command and was hoping you could help me understand how
**to correct this.*
*from the log file *
*INFO: input image orientation is LPS
INFO: input image determinant is 3.51562
fslswapdim
Dear FreeSurfer experts,
I came across failure in mni152reg script. It is related to the fact that my
MNI152 template is installed (via neurodebian package of ubuntu) to the
directory where normal user does not have write permissions (see log file in
the attachment).
I expect that this could be
Hi Bruce,
Thanks thats great to know, I have an ellipsoid fitting function ready for the
job.
I've started the process of getting the occipital flatpatch into MATLAB
following some forums posts, the best route seems to be as follows but i'm
getting an error message.
I can't find anyone posting
the gad will make the dura more likely to be segmented as wm and might
require more manual interventions, but if you are willing to put in the
time it should still be usable.
cheers
Bruce
On Wed, 13 May 2015, Santosh Yadav wrote:
Dear FreeSurfer Experts,
I have a data set (control and pa
I think you want to use flat.[xyz], but I'm not that familiar with the
patch function
cheers
Bruce
On Wed, 13 May 2015, Sarah Finnegan
wrote:
Hi Bruce,
Thanks thats great to know, I have an ellipsoid fitting function ready for
the job.
I've started the process of getting the occipital fla
If you want to look at an interaction between continuous variables, then
create a new continuous variable that is the product of the two and test
whether that is 0
doug
On 05/12/2015 01:46 PM, Sarah Banducci wrote:
> I'm trying to see if two behavioral variables interact (they are
> factors 1 a
Thanks. This has been noted before and fixed. You can get a new version
from here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
On 05/13/2015 07:05 AM, Antonin Skoch wrote:
> Dear FreeSurfer experts,
>
> I came across failure in mni152reg script. It is related to the fac
wow, I have not thought about that code in years. It uses an AR1 with
the bias correction described in Worsley's paper. It bins the AR1 value
into 30 bins to allow for spatial variability and does the whitening in
each set of voxels in a bin.
doug
On 05/12/2015 10:56 PM, Caspar M. Schwiedrzik
Thanks, Doug!
The reason I am asking is that this paper is currently making a bit of
commotion:
*Empirically investigating the statistical validty of SPM, FSL and AFNI for
single subject fMRI analysis*
Eklund, Nichols, Andersson, Knutsson
https://dl.dropboxusercontent.com/u/4494604/article.pdf
No
Antonin,
This is bug in recon-all that will be fixed for the next release. You
can edit your recon-all, adding the lines with a +, to include this fix
via this diff:
set mdir=$SUBJECTS_DIR/${subjid}/mri
set sdir=$SUBJECTS_DIR/${subjid}/surf
+ set tdir=$SUBJECTS_DIR/${subjid}/touch
if (!
I'm registering a subject to cvs_avg35_inMNI152 using mri_cvs_register. My
command is:
mri_cvs_register --mov patient --template cvs_avg35_inMNI152 --m3d
--nocleanup --openmp 8 --keepelreg --hemi lh
Then I'm using applymorph to apply the resulting warp
(combined_tocvs_avg35_inMNI152_elreg_aft
Hello,
>From the standard "fsaverage" subject, I'm trying to map a series of labels
>(?h.oasis.chubs.*) to a group of my own subjects. My end goal is to create
>summary files equivalent to ?h.aparc.stats for each subject. For sample
>commands, I've been looking at the "BA label" section of a su
Dear professor Bruce!
Sorry for bothering you again! I'm about to extract the hippocampus volume
of a group of FS processed patients. Though, I have a few questions without
explicit answers on the Internet.
As recommended on FS tutorials I'm using this commando on the terminal:
"recon-all -s
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