Hi Anna
freeview now checks (in the dev version I believe) if the label has been
sampled onto the surface and won't crash, but you need to use
mri_label2label to sample it onto the surface before loading it onto the
inflated surface in freeview
cheers
Bruce
On Mon, 26 Sep 2016, Crawford,
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a
label on the surface (inflated), it crashed FreeView. I'm not sure why it won't
load there. I noticed this happens with some other ore-made labels as well.
What could be the cause of this?
I also tried doing
what was different? And can you send us the rawavg.mgz for the two cases?
On Mon, 26 Sep 2016, Tamara Tavares wrote:
Thank you Bruce!
Theoretically, I should get the same results if I pass my nii file through
the recon-all command if I converted my dicom/IMA file into a nii using
Slicer4 or
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers
Bruce
On Mon, 26 Sep
2016, Crawford, Anna wrote:
> To create the volume ROI, I found something that said to use:
>
> scuba -v $filename
>
> to then make a new ROI.
>
> I got en error that I could not open scuba. Is
Hello Freesurfers,
I am interested in obtaining the regional volumes of white matter
hypointensities.
What volume would I use a reference for obtaining the 'regions' ? and what
commands would I need to use to obtain these regional volumes ?
?If there isn't an appropriate white matter
Thank you Bruce!
Theoretically, I should get the same results if I pass my nii file through
the recon-all command if I converted my dicom/IMA file into a nii using
Slicer4 or the mri convert command? I did this and I got different volumes.
Thank you,
Tamara
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about
this, or is there some other means that I should be doing not 'scuba'?
Thank you,
Anna
1. It is the signed dot product of the movement vector with the outwards
pointing surface normal of the white matter surface during inflation.
2. Yes, because moving inwards for gyri the dot product is negative.
3. Yes, I think so, although I'm not sure I understand.
4. mris_anatomical_stats
Dear FreeSurfer Team,
I have questions about the sulcal depth.
1) I heard that the output/surf/?h.sulc is showing the sulcal depth.
Is it correct that the sulcal depth measure unit is normalized z-score,
mm? And is it correct that the (-) values of sulcal depth mean gyral region
(green), and
yes, create a volume ROI and you can map it onto the surface using
mri_vol2surf
cheers
Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to
> this and am just trying to figure out how to get the basic process first.)
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to
this and am just trying to figure out how to get the basic process first.)
Eventually, I will want it related to another signal such as the EEG from an
epilepsy subject for example. In that case, it would be the
can you explain what the ROI is supposed to represent? If you can create
it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers
Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> Hi,
>
> I am having trouble figuring out how to create my own ROI. I can visualize
> the
Hi Ruopeng,
When I try to open it, this is part of the error message that appears:
freeview -v 2000_2/mri/T1.mgz 2000_2/mri/brainmask.mgz:colormap=heat:opacity=0.4
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
X Error: BadValue (integer
The FreeSurfer Software License Agreement does not contain any language
explicitly or implicitly preventing commercial usage, however I will
highlight the following text from the License Agreement:
"Any commercialization of the Software is at the sole risk
of the party or parties engaged in
Anyone have any thoughts on this?
On 09/21/2016 04:18 PM, Joel Bruss wrote:
> I have two subjects, subA and subB. subA has a binary ROI mask, native
> space, that I'd like to place in subB's native space. Both subjects have
> been run through all stages of recon, edited, etc. Is there a better
Dear FS experts
I have one concern regarding the license and the Freesurfer usage on
industry.
We are setting up a start-up specialized with the analysis of brain MRI and
we are interested on using FreeSurfer package as our main neuroimaging
tool, due to the large amount of utilities it
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the
anatomical ROI created automatically. How do I create a new ROI?
Thanks,
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to
the white or pial surface, then you can visualize them on the inflated
surface trivially. That is, you can create your ROI on any surface of the
same hemisphere/subject and visualize it on any other
cheers
Bruce
Postdoctoral research associate positions are available in the Department
of Radiology and Biomedical Research Imaging Center (BRIC) at the
University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current
focuses are to better understand the dynamic development of brain
structure,
Hello,
I am trying to create a new surface area on the inflated brain given by
freesurfer using recon-all. I make to create my own ROI that is co-registered
onto this surfer. Ultimately, I want to be able to take information from a
different data source such as EEG and have it co-registered
Hi,
I am having some trouble with white matter editing using control points. I am
placing control points in white matter with intensity <110, and I find that it
seems to have different effects in different slices/subjects, which makes it
hard to develop a general standard for control point
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