Hey Bruce,
Following up with the question can I find any documentation to improve the
segmentation like what are the parameters that needs to be tweaked. Can we
use any seed points to classify and improve the segmentation? How to decide
the thresholds in choosing the parameters to improve the segm
I don't think there is a command to do this. I'd probably do it in
matlab. Info about the coordinates can be found here
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
Each mgz volume has a voxel-to-RAS matrix, if you invert that, and
multiply your RAS you will get the column, row,
Hi,
Could you please let me know the command that takes say, ras coordinates (or a
list of them) and a .mgz as input, and outputs the corresponding voxel values
from the .mgz?
Thanks.
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yes, that sounds right. Does it look correct? That is, are areas 1/4
etc.. in the central sulcus and such?
On Mon, 25 Apr 2016, Trisanna
Sprung-Much wrote:
Not a problem, Dr. Fischl!
In the meantime, could you please confirm that I am opening up a
cytoarchitectonic probability map I have as .
Not a problem, Dr. Fischl!
In the meantime, could you please confirm that I am opening up a
cytoarchitectonic probability map I have as .mnc correctly?
I basically change it to a surface overlay.mgz using mri_vol2surf and then
open it as an overlay with a surface in Freeview. I can then change th
Thank you Eugenio! This worked like a charm.
Wondering now if you could help me troubleshoot running this command on 2 scans
from a single subject (time 1 and time 2) that were processed using the
longitudinal pipeline in version 5.3.
I ran the following:
recon-all -all -s 18512_T1_v5.3_hipp_
Hi Trisanna
yes, but Ruopeng is on vacation to it will be a while
Bruce
On Mon, 25 Apr 2016,
Trisanna Sprung-Much wrote:
Hi there
With regards to this email from March, I cannot seem to be able to change
thresholds of .labels in Freeview. Could this be added as an option?
best wishes
Tris
Hi Anna
if you have dicoms that are T1-weighted and about 1mm isotropic (less than
say 1.3mm in any direction), just give them to recon-all as input and it
will essentially do everything in native space (and will take 12-20 hours
depending on hardware/anatomy)
cheers
Bruce
On Mon, 25 Apr 2
Hi Doug
two aren't necessarily better than one. It depends on your coil/field
strength and amount of motion. In particular, a coronal and a sagittal
will have differential distortions that will blur the average. It might
still help if your data is noisy - it's hard to say a priori, but somethi
Hi there
With regards to this email from March,* I cannot seem to be able to change
thresholds of .labels in Freeview*. Could this be added as an option?
best wishes
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Sun, Mar 13, 2016 at 1:45 PM, Br
Hi,
I'm writing from UChicago to inquire as to what the easiest way to
calculate ventricular volumes is using the segmentation tools. I'm having a
hard time navigating your wiki. If there is a command line protocol for
this listed, can you please refer me to it? Otherwise I may need help
walking t
Hello Freesurfer experts,
We currently acquire two sagittal T1s (136 slices) in our protocol so that we
can take advantage of freesurfer's motion correction algorithm; however, we
would like to add a coronal T1 (196 slices). In order to cut down on scan time,
we are also considering dropping on
Hi Tracula Experts,
How do you determine if a pathway reconstructed well? I've been examining
the merged pathways (/dpath/merged_avg33_mni_bbr.mgz) in freeview,
and if the pathway looked too small when viewing with the default
threshold, I would reinitialize those pathways. Most of the time, the n
nope, but in occipital and perirolandic cortex I couldn't see the
gray/white boundary in your data, so make sure your scans have contrast
there
On Mon, 25 Apr 2016,
Ramtilak Gattu wrote:
Hey Bruce,
These scans are done on 3T Siemens Trio.
Will send you CNR for some of the cases . Are you l
Hey Bruce,
These scans are done on 3T Siemens Trio.
Will send you CNR for some of the cases . Are you looking for any specific
structures in particular.
Thanks
Regards
Tilak
On Mon, Apr 25, 2016 at 12:01 PM, Ramtilak Gattu <
ti...@neurologicstudies.com> wrote:
> Hello Bruce,
>
> Thanks for th
thanks, I had forgotten. Is this 1.5T? I'm a bit concerned about the lack
of contrast in addition to the noise. I guess decreasing the TE will help
this, but you might also try a larger flip. 30 frequently gives us better
T1 CNR than 20 (although it's further from the Ernst angle, and hence
noi
Hello Bruce,
Thanks for the response. I previously mentioned the parameters in the
earlier discussion for the same topic and you have suggested to decrease
the TE and increase the voxelsize to 1.2mm for better SNR. For the
recollection I am again mentioning the complete parameters here-
The par
On 04/25/2016 05:28 AM, Jockwitz, Christiane wrote:
>
> Dear FreeSurfer Experts,
>
> I’ve got a question regarding effect sizes: I did a local gyrification
> analysis using QDEC. I obtained several significant clusters from the
> analysis for whom I would like to calculate some effect sizes.
>
Dear all,
I am creating a hand-drawn label of the Intraparietal sulcus on fsaverge.
When I register it to an individual brain (mri_label2label), the area
is incorrectly registered and comprises adjacent brain structures that
I am not interested in analyzing (specially the neighboring sulci).
I k
A prospective, longitudinal birth mother-offspring cohort study (Growing
Up in Singapore Towards Health Outcomes; GUSTO) study provides a unique
opportunity to investigate 1) gene-environment influence on cognitive and
brain development; 2) the regulation of epigenetic memory on the
development of
Hi Hassan
Doug answered this question - did you not see it? The lh-WhiteSurfArea
is the total surface area of the left hemisphere white matter surface.
It is just a single number, so showing it in freeview doesn't make sense.
If there is something specific you are trying to accomplish let us k
Dear FreeSurfer Experts,
I've got a question regarding effect sizes: I did a local gyrification analysis
using QDEC. I obtained several significant clusters from the analysis for whom
I would like to calculate some effect sizes.
On the website/helpline, I saw that fscalc might do this job. Ther
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