Dear Bruce,
Thank you very much for taking your time to have a look at my data, which I
just uploaded to the transfer/incoming/ folder.
The specific coordinates are: RAS 4, -73, 27
In addition, I have a similar problem more anterior too (RAS 32, 39, 2.5).
Thanks again for your help!
S
Thank you so much! I understand what's the problem and I will make my
custom ctab file.
Last question, about the annot files, is it possible with freesurfer to
create a mask with the annot or the label files in which the value 1 is
assigned to the region and 0 to the rest of the brain?
Thanks aga
yes, you can use a label for this (we use the ?h.cortex.label for this
purpose routinely to remove non-cortical stuff)
On Tue, 5 May 2015,
Francesca Strappini wrote:
Thank you so much! I understand what's the problem and I will make my custom
ctab file.
Last question, about the annot files, i
Hi Annie,
Please cc the freesurfer list when you reply because there might be
other people more qualified to answer your question.
Based on what you are saying, I think you can first use mri_surf2surf
(with the "sval-annot" flag) to transform the 2011 functional networks
.annot file from fsaverag
Thank you! Do you know which function should I use?
Best
Francesca
2015-05-05 15:30 GMT+03:00 Bruce Fischl :
> yes, you can use a label for this (we use the ?h.cortex.label for this
> purpose routinely to remove non-cortical stuff)
>
> On Tue, 5 May 2015, Francesca Strappini wrote:
>
> Thank yo
Sorry, just to be clear, I meant how can I create a mask on the surface in
which at each vertex is assigned a value, 0 or 1.
I need to create this mask for exporting the freesurfer labels into SUMA
and ultimately to extract the time series from each vertex.
Thanks
Francesca
2015-05-05 16:06 GMT+0
Hello,
I want to compare mean lGI values between two groups in a spherical ROI centred
on a specific MNI coordinate. I have been running group comparisons of
gyrification index so far in Qdec but can’t see how to build the ROI that I
need nor how to analyse lGI values within a specific ROI.
Hi all,
What command would I use to apply the aparc labels to a different surface
(e.g. to $h.ratio.mgh)??
The ratio file was created as follows:
mri_vol2surf --src ${nu_mgz} --projfrac +0.35 --surf white --hemi lh
--out ${subj_dir}/mri/lh.white.projfrac.pos35.mgh --regheader ${subject}
--nor
Hello FS experts,
I submitted this question yesterday but never heard back. Any thoughts?
Thank you!
Gabriella
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella
Sent: Monday, May 04, 2015 3:03 PM
To: freesurfer@nmr.mgh.ha
Yes,
if this is in the long, you also need to add the -long …. stuff
Martin
> On Apr 28, 2015, at 12:46 AM, prasser wrote:
>
> Thanks for your response, not sure if I've quite got it yet.
>
> So, after the surfaces are done and we update/edit the the aseg.mgz with say,
>
> recon-all -surfseg
Hi Sanne,
this is for a longitudinal analysis? Are you doing the 2 stage approach (first
reduction to a single number per subject, e.g. the atrophy rate per year, then
a cross sectional analysis)?
In that case I don’t know why it is not working. Your Y is the thickness rate,
and the 6 columns
Hi Freesurfers,
I've performed recon-all -all on a subject and found that some of the cortex is
missing. I ran "recon-all -skullstrip -wsthresh 30 -clean-bm -no-wsgcaatlas -s
sub296.fs" and the cortex appeared, so I added control points in hopes of FS
recognizing the cortex, but I got the fol
Hi Marie:
I just had another problem with the LGI processing. Here is the log:
thanks,
Alan
[alanf@micc FreeSurfer_5.3]$ recon-all -s Asperger1 -localGI
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
Current Stamp: freesurfer-
Hi,
My name is Fabio, I am from university of Sao Paulo, and we have a few
brains that we wish to try running on freesurfer that are already fixated
and we were not captured the way the current ex vivo protocols suggests.
I have already tried it once, and the segmentation weren't quite good,
howeve
Dear freesurfer,
I tried using kvlThresholdImage on a MacOSX 10.10.2, X version XQuartz
2.7.7 (xorg-server 1.15.2), and freesurfer version 5.3, and I get the
following message:
kvlThresholdImage subj01/mri/orig/orig.mgz
0
2370
X Error of failed request: BadWindow (invalid Window parameter)
what are you trying to mask?
On Tue, 5 May 2015, Francesca Strappini wrote:
Thank you! Do you know which function should I use?
Best
Francesca
2015-05-05 15:30 GMT+03:00 Bruce Fischl :
yes, you can use a label for this (we use the ?h.cortex.label
for this purpose routinely to remov
you can just create a label file I guess. What input does SUMA take?
On Tue,
5 May 2015, Francesca Strappini wrote:
Sorry, just to be clear, I meant how can I create a mask on the surface in
which at each vertex is assigned a value, 0 or 1.
I need to create this mask for exporting the freesurf
Hi Jessica
something has gone terribly wrong with the segmentation. What is the
input image you used? What does the wm.mgz look like over the brain.mgz?
cheers
Bruce
On
Tue, 5 May 2015, Jessica Lynn Hanson wrote:
Hi Freesurfers,
I've performed recon-all -all on a subject and found that
Hi Dr. Schaer,
Jon checked the dates and assured that LGI was run after autorecon. We are
still encountering this issue. Thank you for your help,
Skyler and Jon
Sent from my iPhone
Begin forwarded message:
From: Jon Alan Wieser mailto:wie...@uwm.edu>>
Date: May 5, 2015 at 1:38:31 PM CDT
To: S
I'm trying to mask a time series dataset that I mapped to the surface in
SUMA (surface created with freesurfer and imported into SUMA). I think the
input should be in the .dset fomat (region mapped to the surface). The
problem is that when I save my label the annotation file has only a list of
vert
Hi Skyler,
You can run:
mris_info lh.pial
which will give you the number of vertices of the surface (vertices)
and
mri_info lh.pial_lgi
which will give you the number of vertices for which the LGI has been computed
(under dimensions)
If the two numbers don't match, it means that the LGI has no
sorry, I think this may be a question for the SUMA people - I don't know
what .dset format is. Are you going to do the masking within SUMA? I'll cc
Ziad so he can chime in.
cheers
Bruce
On Tue, 5 May 2015, Francesca Strappini wrote:
I'm trying to mask a time series dataset that I mapped to t
Can you send me the new terminal output (and attach your fsgd file)?
doug
On 05/04/2015 08:48 AM, Sanne Oostermeijer wrote:
> Thank you for answer Douglas.
>
> I have indeed tried to run the analysis by demeaning our covariate, but
> unfortunately I get the same error (matrix is ill-conditioned
Does SUMA support GIFTI and provide a utility to convert between its
formats and GIFTI? I was also wondering what a .dset was and how to get
it into GIFTI so it could be easily used across software platforms.
Thanks,
Matt.
On 5/5/15, 5:30 PM, "Bruce Fischl" wrote:
>sorry, I think this may be
Hi Doug,
I want to do volume based analysis using FSFAST using the FC seed as a task
regressor. I ran the following command lines:
1. preproc-sess -s ${i} -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd
bold -per-run
2. fcseed-config -segid 1024 -fcname L_Precentralgyrus.dat -fsd bo
Dear FS experts,
For my research proposal, I would like to visualize my 5 ROIs (e.g.,
superior temporal cortex, medial temporal cortex) in the Destrieux Atlas
(or others) before I start the analysis. I want each region to be shown in
a different color.
Would you kindly explain how to do it?
Al
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