Hello, Group,
I have a hard time to register the functional ROIs to the exact location
(x,y,z) on thickness map. I can't find articles that register the fsl result
onto freesurfer thickness map and then do the ROI analysis. Could someone
kindly list some references for me? I appreciate if anyo
Dahlia,
Try again now, I just fixed it.
Nick
On Fri, 2008-09-12 at 12:21 -0700, Dahlia Sharon wrote:
> Hi,
>
>
>
> I ran recon-all, and it exited with an error at this command:
>
>
>
> mris_volmask --label_left_white 2 --label_left_ribbon 3 --
> label_right_white 41 --label_right_ribbon
Hi all,
FYI, this same problem has been bugging me for several months. Most
ATI chipsets have a nice driver installer bundle that, once installed,
will let you run tksurfer without a problem. However, this particular
chipset, the ES1000, which is the chipset on Dell PowerEdge servers,
is
Hi,
I ran recon-all, and it exited with an error at this command:
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white
41 --label_right_ribbon 42 --save_ribbon --save_distance subj10
The error message reads:
mris_volmask.bin: error while loading shared librar
Hi Matt,
the Segonne paper is the current skull stripping (the hybrid one), although
it's evolved somewhat since then (unpublished). The segmentation is both
those papers (the first one is the segmentation methodology, the 2nd is the
addition of a nonlinear warp), plus the more recent one with
Hi Bruce,
for sure, I didnt expect it to all be in one place!
For example, what I believe are the original papers (Neuroimage 9 1999,
and the 1993 Cognitive Neuroscience paper), describe the first method,
then we have all the other subsequent papers. So for example, does the
current methodolo
Dear Mr or Ms,
My computer was installed with Freesurfer v4.0.3,centos4,
To make an average surface,I launch "make_average_subject" command,
I come across an error :
Processing subject 25/52 sh45 ...
Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg
Segmentation fault (core dumped)
Dear Mr or Ms,
My computer was installed with Freesurfer v4.0.3,centos4,
To make an average surface,I launch "make_average_subject" command,
I come across an error :
Processing subject 25/52 sh45 ...
Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg
Segmentation fault (core dumped)
It corresponds to the signal change, which is more-or-less A-fixation,
but not exactly. The percent signal change is in cespct.
doug
Reza Rajimehr wrote:
Hi,
For a stimulus condition 'A' and a fixation condition, does the ces file
for the contrast 'A - fix' correspond to the % signal change
You can also skip the 1st two steps and just convert aparc+aseg.mgz to
MNI with mri_vol2vol (make sure to use the --interp nearest flag). Then
look for voxels with values 1030 (left STG) or 2030 (right STG).
doug
Bruce Fischl wrote:
Hi HweeLing,
I think the aparc.a2005s has the STS labeled
Hi Matt,
the methodologies are described in those papers. Sorry, I don't think
there's any one or two paper summary - it's just too much stuff over the
years (topology correction, segmentation, surface analysis, morphing,
etc).
Bruce
On Fri, 12 Sep 2008, Matt Clarkson wrote:
Dear ever
You can use mri_label2vol and spec
$FREESURFER_HOME/average/mni152.register.dat as the registration file.
Cherif Sahyoun wrote:
Hi,
I'd like to morph ROIs drawn on the fsaverage surface onto the MNI152
volume. Any ideas on how to do it?
Usually I'd mri_label2label and then mri_label2vol, but
Dear everyone,
Hopefully someone can help me. If I do "recon-all --help" i can see a
list of 31 steps for the main cortical thickness pipeline. Does anyone
have a list that links each of the 31 steps to the most current
methodology paper?
I've been reading most of the methodology papers re
Hi,
I'd like to morph ROIs drawn on the fsaverage surface onto the MNI152
volume. Any ideas on how to do it?
Usually I'd mri_label2label and then mri_label2vol, but I don't think there
is a surface version of MNI152, is there?
Thanks!
Cherif
---
No problem. What I would do is create a surface-based label file with the
peak in each subject, then use mris_spherical_average to generate an
average label (this will be in spherical coords). A typical command line
would be:
set average_subject=fsaverage
mris_spherical_average -osurf sphere -
Hi Bruce,
Basically I have data from 45 subjects, and I would like to show the
variability in the location of the individuals peak activation. They are
all on the ventral surface, and are in occipitotemporal sulcus and
fusiform gyrus - so ideally I'd like to use the inflated brain as it
would
Hi HweeLing,
I think the aparc.a2005s has the STS labeled in it, so you should already
have what you need in individual space. You could use mri_annot2label,
mri_label2vol and mri_vol2vol to transform this into MNI if you need to.
cheers,
Bruce
On Fri, 12 Sep 2008, Hwee Ling Lee wrote:
Hi Keith,
this is inevitable when sampling from the volume onto the surface,
particularly if the volume maps are blurry. Then a single volume blob will
intersect e.g. two banks of a sulcus and show up as two distinct blobs.
cheers,
Bruce
On Thu,
11 Sep 2008, Keith Duncan wrote:
Hi FS ex
Hi Keith,
I guess you could write your cross locations into an annotation file then
they would be displayed as small colored patches. I'm not sure which
figure you are referring to, or exactly what you're trying to do though.
Bruce
On
Fri, 12 Sep 2008, Keith Duncan wrote:
I've just read Fi
I've just read Fisch et al 2007 (Cerebral Cortex) where Figure 1 (I
think made in tkmedit) shows canonical slices with small green crosses -
is there a way to do a similar thing (preferably not by placing the
crosses manually) on the inflated brain?
Thanks again,
Keith
___
Hi All,
I was looking for methods to create a superior temporal sulcus
mask (upper and lower boundary).
>From my understanding, Freesurfer does a pretty good job in labeling the
sulcus, hence I was wondering if there are possible ways to write the
particular ROI as a mask image for each individua
the average subject is mostly for visualization, so I wouldn't think it
would matter that much.
cheers,
Bruce
On Fri, 12 Sep 2008, Zhangyuanchao wrote:
Are the average subjects generated by different version of Freesurfer differ
greatly?
I obtained the cortical thickness,lGI using Freesurfe
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