Dear FreeSurfers,
I have data has been recon-all analyzed. I would like to compare the
symmetry of function/structure property between LH and RH, such as cortical
thickness. I already know that the vertices in the left hemisphere are not
correspond to vertices in the right hemisphere. I would like
Hi Maria,
You can display a single label (or labels) in tksurfer by loading the aparc
annotation onto fsaverage; then, simply click on the label you're interested
in, and click File, then Label, and Save Selected Label. This will let you save
out a single label from aparc, which can these easil
Are you sure that *all* are 0? By passing it FreeSurferColorLUT.txt, you
force it to report hundreds (or thousands) of ROIs which are not
represented in the aparc+aseg.mgz. Also, try removing --seg-erode.
On 09/18/2014 04:43 PM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your email.
>
>
Dear Doug,
Thank you for your email.
The registration overlap looks reasonable. Thank you for considering this
question.
Best wishes,
Sal
On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve wrote:
>
> When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look reasonable? Does
> it overlay correc
The only way I know is to break the annotation into labels
(mri_annotation2label), then creating a new annotation with only the
labels you want (mris_label2annot). If you only want one label, then you
don't need to create a new annotation
doug
On 09/18/2014 03:11 PM, Maria Kharitonova wrote:
>
Have you run mri_glmfit-sim? It will create labels (ie, annotations) of
the clusters as well as run mri_segstats to get means in each cluster
for each subject. Try that link now
doug
On 09/18/2014 12:15 PM, Celine Louapre wrote:
> Hi Doug and FS team
>
> I did glm analyses using mri_glmfit, and
This is a bug in mris_preproc. A work-around is to add --srcfmt mgh as
the last argument. In the mean time I'll fix mris_preproc
doug
On 09/18/2014 11:32 AM, Lars M. Rimol wrote:
> Hi,
>
> I get the following error message when running mris_preproc, and I'm
> wondering what file is it looking
For each vertex, the col, row, slice in the mdi is computed based on the
registration. The value from this voxel is extracted; the default is
nearest neighbor but this can be changed with --interp trilin
doug
On 09/18/2014 10:52 AM, Nicholas Heugel wrote:
> I looked over the documentation but c
The easiest way is to run mri_glmfit-sim from the command line on the
QDEC output folder. It will automatically correct for multiple
comparisons and create tables. See the tutorial (and other posts along
this line).
doug
On 09/18/2014 05:56 AM, elisa veronese wrote:
> Dear FreeSurfers,
>
> can
Can you get it to display correctly on the pial surface in conformed space?
On 09/17/2014 08:04 PM, Zachary Greenberg wrote:
> Hello Freesurfer experts,
>
> I am having a tough time getting my pial surfaces into the correct
> anatomical space. I work with ECoG Patients, so we have pre-implant
>
0.5 is pretty good for fMRI. If it looks good visually, then I would not
worry about it further
doug
On 09/17/2014 09:25 AM, lorenzo pasquini wrote:
> Dear Freesurfer users,
> I have used the command bb_register to automatically register raw fMRI
> data on the anatomy. The output looks visually
When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look reasonable?
Does it overlay correctly on the T1.mgz?
doug
On 09/14/2014 11:40 PM, Salil Soman wrote:
> Thank you Doug. I am having trouble with extracting statistics using
> this method.
>
> I am able to use bbregister to get a transform
Yes, that can be helpful. As a caution though, the overall quality may appear fine, but things like topology correction errors can still occur and will be quite local. Thus, they would easily be missed if the density of your screenshots isn't high enough.
Personally, I find it only margi
Try out Freesurfer's QAtools. It still isn't "automatic", but you can
get a bunch of screenshots and view them all on an html page.
On 09/18/2014 11:42 AM, Harms, Michael wrote:
Hi Ezra,
I'd love to hear otherwise if someone has established some robust
signal processing approaches to do this
Hi Doug and FS team
I did glm analyses using mri_glmfit, and I was trying to plot the
individual values in the population for a specific significant cluster.
However I am not sure how to extract individual values from the entire
cluster. (note that the concatenated surface used as input for the gl
Hi Ezra,
I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion. It is time consuming, but you have to put eyes on the
data.
cheers,
-MH
--
Hi,
I get the following error message when running mris_preproc, and I'm
wondering what file is it looking for?:
Reading curvature file
/usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null)
MRISreadCurvature: could not open
/usit/abel/u1/rimol/subjects/long/long_v0v2_
Hi Nicholas
mri_vol2surf has options that lets you control its behavior. It can do
various types of sampling (e.g. averaging within the cortical ribbon, point
sampling at a specified distance or percentage, etc)
cheers
Bruce
On Thu, 18 Sep
2014, Nicholas Heugel wrote:
I looked over t
Dear Freesurfer and DTI experts,I will start some analyses with DWI data, but I have some doubts about it:1) I have data with 5 different acquisition protocols, so, I'm not sure if the standard pre-processing protocol (like eddy-current compensations the reorientation of the vectors and the intra-s
Dear Freesurfer Users,
I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio
scanner that I would like to run through recon-all to get cortical
thickness values. However, some of the MPRAGE scans are contaminated by
subject motion, but the extent of this varies from scan to scan
I looked over the documentation but can;t seem to find what I am looking
for. How exactly does the function project the mdi data onto the surface?
What method is it using to accomplish this, is it just projecting to the
nearest neighbor or is there something more complex occurring. I ask
because
Dear FreeSurfers,
can anybody tell me if there is a way to export results in form of table
(or text file) from the QDEC GUI after having performed analysis on
thickness, area, volume, etc etc... ?
I mean, is the infomation regarding the significant clusters saved in table
format?
Thank you.
Best
Dear FreeSurfer experts,
I understand that
> freeview -v brain.nii.gz -ss screenshot
takes the screenshots and quits the freeview.
Regarding this, I have the following two questions.
(1) Is it possible to suppress the redundant GUI flashing?
It is really a pain when many images are batch-proces
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