Is there any paper that you can share that can explain why recon-all is not
suitable for neonates brain apart from atlas.
Sarbani
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei
Sent: 06 July 2017 2
Dear FreeSurfer experts,
I have figured out what the problem is, however I do not know how to solve it.
Apparently the homogeneity function within the lme_mass_RgGrow function does
not recognize the voxels as homogenous if they have zeros in all columns
because the correlation coefficient is Na
Hi all,
Do you need to edit the wm mask where the internal structures shown in the
aseg are? are the structures supposed to be covered entirely with the wm
mask?
Karla
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because neonate geometry and lack of myelin cause the brains to look so
different from what many of our algorithms expect.
cheers
Bruce
On Fri, 7 Jul 2017, Das S. wrote:
> Is there any paper that you can share that can explain why recon-all is not
> suitable for neonates brain apart from atla
Hi Gabor
whether it "matters" is really a question of what you want to do with the
data. The chiasm is pretty small and won't change much
cheers
Bruce
On Fri, 7 Jul 2017,
Gabor Perlaki wrote:
Dear all,
Freesurfer 6 creates pial and white matter surfaces around the optic chiasm
in some of
Hi Karla
you shouldn't have to worry about the wm.mgz in those regions if the aseg
is accurate.
cheers
Bruce
On Fri, 7 Jul 2017, Karla Rivera Figueroa wrote:
Hi all, Do you need to edit the wm mask where the internal structures shown
in the aseg are? are the structures supposed to be cover
Hi Team,
I'm attempting to extract cortical thickness values for a region-of-interest
(ROI) defined in volume spacesubject for PiB MRI.
I got the below mentioned error while computing the stats value
cwd
cmdline mri_segstats --seg
freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh --in
Hi Kaley
are you using the "recon edit" tool in freeview?
cheers
Bruce
On Fri, 7 Jul 2017, KALEY E
ELLIS wrote:
Dear FreeSurfer Developers,
We are attempting to make manual white matter edits to our subjects. The
edits are saving; however, after running with recon-all, the WM surface doe
Hi Sarbani,
Please see this paper for more information:
https://www.ncbi.nlm.nih.gov/pubmed/25741260
Emma
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Das S.
Sent: Friday, July 7, 2017 4:58:39 AM
To: Freesurfer support list
Subject: Re: [Freesurfe
Thank you for the clarification.
Have a nice weekend,
Karla
On Jul 7, 2017 10:16 AM, "Bruce Fischl" wrote:
Hi Karla
you shouldn't have to worry about the wm.mgz in those regions if the aseg
is accurate.
cheers
Bruce
On Fri, 7 Jul 2017, Karla Rivera Figueroa wrote:
Hi all, Do you need to ed
?When I use a script like this,
mri_glmfit --y ces.nii --wls cesvar.nii --osgm --frame-mask masks.nii --surface
fsaverage rh --glmdir my-glm2.wls --nii.gz?
using the individual binary masks for all the subjects, the command seems to
revert to using mask.nii, the single mask that was averaged ov
Add --no-prune
On 7/7/17 11:38 AM, Sadie Marvel wrote:
When I use a script like this,
mri_glmfit --y ces.nii --wls cesvar.nii --osgm --frame-mask masks.nii
--surface fsaverage rh --glmdir my-glm2.wls --nii.gz
using the individual binary masks for all the subjects, the command
seems to r
du/mailman/listinfo/freesurfer
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Can you send your command and log file?
On 6/16/17 7:37 AM, Magnús Ingvi wrote:
Hi, I've been trying to run glmfit_sim on a glm analysis with data in
the AVG_35_CVS space but it doesn't seem to finish (tried almost two
weeks). Does anyone have an idea what might be going on here? I used
mc_fu
Can you send the full terminal output?
On 6/27/17 4:15 PM, SudEEpti wrote:
I tried the following, but the program seems to seg fault. No output
files are created. Please let me know what you think I might be
missing. Thank you!
>mri_gtmpvc --i pet.nii.gz --seg gtmseg.mgz --reg reg.lta --o $P
And the same process worked for thalamus and amygdala? If so, then I
don't know what is going wrong. Try doing the visualization in freeview.
Also see if the amyg/thal seem to be in the right place relative to
brainstem when you visualize all of them together.
On 6/25/17 9:31 AM, Dr Sampada S
In that mri_segstats command, you will get a column for everything that
is not in a cluster as well as for each cluster. Make sure that you are
using the correct column. The other thing you can do is to run the post
hoc test in matlab, somthing like
y = load('file.stats');
X = load('Xg.dat');
No, this is just for visualization purposes (I assume)
On 7/6/17 8:46 AM, miracoo...@gmail.com wrote:
Thanks doug. Do I need to include a flag in gtmseg to change the colour?
Best.
Paul
Sent from my BlackBerry 10 smartphone.
*From: *Douglas Greve
*Sent: *Thursday, July 6, 2017 12:12 AM
*To: *f
How did you create the segmentation? You can change the shape of the seg
with mri_surf2surf --reshape 6 --s fsaverage --hemi lh --sval seg.mgh
--tval seg.reshape.mgh
On 7/7/17 10:15 AM, M Janani wrote:
Hi Team,
I'm attempting to extract cortical thickness values for a
region-of-interest (R
Dear FreeSurfer mailing list,
I've got two questions regarding the freesurfer GLM analysis.
1. I am trying to run mri_glmfit on the cortical thickness of a dataset
that has a few interacting factors of unequal levels.
For example, my dataset may have groups A, B, C, and D. Within the groups,
subj
On 7/7/17 1:58 PM, Yann Ying Chye wrote:
Dear FreeSurfer mailing list,
I've got two questions regarding the freesurfer GLM analysis.
1. I am trying to run mri_glmfit on the cortical thickness of a
dataset that has a few interacting factors of unequal levels.
For example, my dataset may have
Hi Aly, it is not creating the path correctly, not sure why. Can you run
it again with --debug as the first option and send me the terminal output?
doug
On 7/1/17 1:57 PM, Aly Negreira wrote:
Hi Freesurfer Community,
I'm using FsFast on my dissertation data and trying to run a monte
carlo
not sure, a pointer to the page would make it easier. probably it is the
T1 image of the mni152 that is distributed with FSL and SPM
On 7/3/17 1:33 AM, M Janani wrote:
Hi Team,
Currently I’m working on ROI analyses. I saw one
article related to VolumeROICorticalThickness in
sorry, that is not possible with the tools as they are. I had no idea
someone would be trying to do something like this when I programmed it!
I'll keep it in mind if I make modifications ...
On 7/1/17 6:54 AM, Victor Montal Blancafort wrote:
Dear Doug,
We are trying to compute partial volume
On 6/19/17 10:08 PM, Livia Liu wrote:
Dear FS experts,
I are analysing longitudinal data - the difference of the cortical
thickness, surface area and volume between 2 groups (1 and 0) with 2
time points for each group (0, 1 --all the same time interval: a month).
I followed the page
http
You can create individual labels with mri_annotation2label from the
fsaverage annotation. The label is a text file with coordinate in it.
The coordinates will be MNI305 space. You can read these into matlab
with read_label.m. These will need to be converted to MNI152. See
http://surfer.nmr.mgh.
Hello,
I am testing my FreeSurfer installation by doing the practices shown on the
page. Regardless of command-although I managed to convert the sample to nifti
format- this error on line 2 shows up. Can anyone explain what that could be
caused by and point me in the right direction to fix it?
Thanks Dr Douglas for bringing that out. If I remember correctly these
structures did align when I viewed it using freeview. Will send the
pictures later to confirm. Also these images had a good overlay with
fsaverage image using tkmedit tool. Only that the resolution was not good
with fsaverage th
Hello everyone,
I'm pretty new to FS and can't seem to find the solution for my problem.
I am trying to write whole-brain vertex-wise cortical thickness (CT) data
from each participant into ascii files. In my original analysis, each
participant's average CT in clusters derived from a whole-brai
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