Hi,
I ran into 2 problems related to tracula.
1. trac-all -bedp command exits with following message.
WARN: Running FSL's bedbost locally - this might take a while
> WARN: It is recommended to run this step on a cluster
> bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri
> s
Hi Michelle,
the odd shaped shards and triangles usually means you recreated the
surfaces after flattening, so the flattening needs to be redone. The swirls
can be a number of things, possibly incorrect cuts. If you want to upload
an example I'll take a look.
cheers
Bruce
On Thu, 6 Oct 20
Hi all :
I'm performing general linear model (GLM) analysis in the surface,the
attachments above are FSGD file and contrast files(the last three
attachments).i wonder if my contrast files are correct.
the attachment named diff-C-H-thickness.txt is about difference between C
and H and t
Hi Judit,
1. If you can run bedpostx directly then you should do:
bedpostx /usr/local/freesurfer/subjects/C001/dmri
Note that this dmri directory and the one you tried to run
bedpostx_single_slice.sh on are different, so I'm not sure which location
is the right one where your data is, but in
Dear FreeSurfers,
This is a question I posted yesterday and I got not answer yet. I am trying to
re-sample a NIFTI image (obtained after MRIcron conversion, from a dcm image)
in Freesurfer with a scale factor of 2.
I know about mri_convert with the option -rt but this doesn't give me any
opti
Hi Antonella,
this would be pretty easy to do in matlab I guess. Why do you want to do
it? Do you really just want to drop every other slice? Do you want to
change the in-plane resolution?
Bruce
On Fri, 7 Oct 2011,
Antonella Kis wrote:
>
> Dear FreeSurfers,
>
> This is a question I posted
I have data from 100 monkeys and I need to compare cortical thickness
among two groups.
In the wiki page there is an entry MonkeyData that has a set of
scripts which break-down the steps needed, unfortunately I'm having
trouble with this scripts and FS 5.1
Are there an updated version of those pr
Hi Pedro,
On Oct 7, 2011, at 9:02 , Pedro Paulo de Magalhães Oliveira Junior wrote:
> I have data from 100 monkeys and I need to compare cortical thickness
> among two groups.
>
> In the wiki page there is an entry MonkeyData that has a set of
> scripts which break-down the steps needed, unfort
Hi,
I would appreciate if you can help me with the following question: what should
be the range values on the QDEC and/or GLM color scale if the cwp values for
the cached clusters at thresh 2 and cwpvalthresh .99 are between 0.4465 and
0.9710? Also, I wonder if there is a way in QDEC to
Dear FreeSurfers,
I am following the cut plane steps on the freesurfer wiki
(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch).
I marked a closed areas, press the 'cut closed line' button, left-click
in the area, and then press the 'fill uncut area' button. Upon click
Dear Freesurfers,
I am trying to describe how freesurfer conducts it's retinotopy analysis to
make the polar, eccen and fieldsign maps.
Is there a detailed description of this somewhere? I can't seem to find an
indepth description on the wiki.
Thanks.
Michelle
Dear FreeSurfers,
In aparc+aseg file, each segmented or parceled region seems to be labeled by
its own intensity (e.g. the intensity is 53 in the right hippocampus, 10 in
the left thalamus...) when I see it on FSL viewer.
Where can I find the table that shows the relationship between the intensi
Hi Shige - See $FREESURFER_HOME/FreeSurferColorLUT.txt.
a.y
On Fri, 7 Oct 2011, Shigetoshi Takaya wrote:
> Dear FreeSurfers,
>
> In aparc+aseg file, each segmented or parceled region seems to be labeled by
> its own intensity (e.g. the intensity is 53 in the right hippocampus, 10 in
> the left
I am using recon-all command to process some analyze images. But it seems
that this command does not work for all .img images. For example, I have an
image with the following information:
256x256x124
0.7mm x 0.7mm x 1.5mm
data type: uint8
description:
position:000
file orientation:
1 0 0
0
Hi Jie,
it should be ok. We typically don't recommend this type of "french fry"
voxel with one dimension beting almost 4 times as long as the others. You
are usually better off getting closer to isotropic. That said, if the SNR
is good enough try giving it to recon-all. One thing to be wary of
Hi All,
I have some functional beta maps normalised to the T1 template using spm8 and I
am wondering how to map them onto the fsaverage surface ?
In native subject space, I pipe a functional scout image into bbregister to get
a registration matrix which is then used to map volumetric beta maps
Hi Bruce,
I've uploaded a tar file called umali_fieldsign_swirl.
It contains two directories one anatomical and the other retinotopy both
from the same subject 29:
ld29 which contains the recon-all output anatomical data
sj29 which contains all the retinotopy data. the subjectfilename says ld29
Hi Ri
if you have them on the surface using the bbregister registration you can
use mri_surf2surf to map them to fsaverage (or any other subject).
cheers
Bruce
On Fri, 7
Oct 2011, Ritobrato Datta wrote:
> Hi All,
>
> I have some functional beta maps normalised to the T1 template using spm8 and
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