Hi all,
I'm trying to run Monte Carlo simulations on cortical thickness data I got
using mri_glmfit, but I'm running into some errors.
1) I used the command
mri_glmfit-sim --glmdir lh.thickness.fwhm20.diagnosis_scanner.dods.glmdir/
--cache 2.0 pos
The error I receive says cannot find
Dear FreeSurfers,
I have a question concerning pctsurfcon and subcutaneous fat. The first
step in the Freesurfer processing pipeline is intensity normalisation,
which assumes that high intensity signal is due to white matter and uses
this as a reference point. However this happens prior to
Hi Nenad
we actually do the intensity normalization mutliple times, the final one
on the skull stripped images. We do try to distinguish even if the skull
is in the image using connectivity constraints.
cheers
Bruce
On Fri, 11 Apr 2014, N.
Medic wrote:
Dear FreeSurfers,
I have a question
yes, that would help
On Fri, 11 Apr 2014, Xuelong Zhao wrote:
Addendum to the previous post:
Can I use lh.orig as the input surface instead of lh.inflated?
Also, I ran the command you suggested (I changed -w flag to 10 and used lh.orig
as the
input surface):
mris_sphere -w 10 lh.orig
Hi all,
is there a way, to install only freeview not the whole Freesurfer package (on
Mac OS X). Or, alternatively, can somebody please tell me what I can safely
remove after installing the whole package to be able to still run Freeview, but
save the maximum of hard disk space?
I do all
probably all you need is the freeview binary and the license file, but
Ruopeng can confirm
Bruce
On Fri, 11 Apr 2014, Janosch Linkersdörfer wrote:
Hi all,
is there a way, to install only freeview not the whole Freesurfer package (on
Mac OS X). Or, alternatively, can somebody please tell me
Hello FreeSurfer Experts,
On review of stats file in FreeSurfer a tumor volume is reported. How is
tumor segmentation achieved by FreeSurfer?
Thank you
Mohammed Goryawala, PhD
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I think we need to distribute it with a license for NIH-accounting
purposes. The license is free and trivial to get so it's not really much
of a hardship
On Fri, 11 Apr 2014, Ruopeng Wang wrote:
I have a stand-alone FreeView build for Mac that doesn't even need license
file to run. Can we
OK. I'll put in license checking.
On 04/11/2014 10:57 AM, Bruce Fischl wrote:
I think we need to distribute it with a license for NIH-accounting
purposes. The license is free and trivial to get so it's not really
much of a hardship
On Fri, 11 Apr 2014, Ruopeng Wang wrote:
I have a
Dear Louis (and Bruce),
So I have run
recon-all -skullstrip -clean-bm -gcut -subjid subjid
on my subjects where remaining pieces of dura after a normal recon-all got
included into pial surface. I am having a look at the result before
continuing with autorecon2 etc.
Results are not yet
On 04/11/2014 02:52 AM, Gautam Tammewar wrote:
Hi all,
I'm trying to run Monte Carlo simulations on cortical thickness data I
got using mri_glmfit, but I'm running into some errors.
1) I used the command
mri_glmfit-sim --glmdir
lh.thickness.fwhm20.diagnosis_scanner.dods.glmdir/ --cache
That should have been --nreps 1 (not 100:)
On 04/11/2014 11:04 AM, Douglas N Greve wrote:
On 04/11/2014 02:52 AM, Gautam Tammewar wrote:
Hi all,
I'm trying to run Monte Carlo simulations on cortical thickness data
I got using mri_glmfit, but I'm running into some errors.
1) I used
Hi Markus,
You can try running mri_gcut with a slightly higher T value, default is
0.4.
command would be something like (running from within subject's mri dir):
mri_gcut -T 0.5 T1.mgz brainmask.gcuts.T-0.5.mgz
Carefully inspect the output, overlaid as a heatmap on the T1 and/or
previous
Hi Markus
I'm not really sure. I'll cc Mike Chee whose lab the graph cuts stuff was
developed in
Bruce
On Fri, 11 Apr 2014, Markus Gschwind wrote:
Dear Louis (and Bruce),
So I have run
recon-all -skullstrip -clean-bm -gcut -subjid subjid
on my subjects where remaining pieces of dura
Hi Jinnan
do you mean track from a subcortical structure to cortex and show the
targets on the surface? I believe that can be done with the FSL tools in
combination with our surfaces. Perhaps Anastasia can comment?
Bruce
On Fri, 11 Apr
2014, Douglas N Greve wrote:
Hi Jinnan, I don't know
I've just created the following docs for mri_mcsim
doug
mri_mcsim
--o top-output-dir
--base csdbase
--surface subjectname hemi
--nreps nrepetitions
--fwhm FWHM FWHM2 FWHM3 ...
--fwhm-max FWHMMax : sim with fwhm=1:FWHMMax (default 30)
--avgvtxarea : report cluster
Thanks Louis!
Great. It seems I need -T 0.65. That looks fine.
Is it necessary
- to name the modified brainmask.gcuts.T065.mgz?
- and keep both brainmask.mgz and brainmask.gcuts.mgz in the mri folder?
And then continue with
recon-all autorecon2 autorecon3 -s subjectid
Is that correct?
Thank
Good to hear. That was just a naming convention to keep track of how each
version was generated.
To continue, all you need to do is rename the good brainmask (generated
with the modified gcuts command) to brainmask.mgz.
-Louis
On Fri, 11 Apr 2014, Markus Gschwind wrote:
Thanks Louis!
Hi all,
I am trying to extract vertexwise surface area values in an ascii files. For
that I am doing
mri_surf2surf
--hemi ?h --srcsubject subject dir area --src_type curv
--trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv
mris_convert -c XYZ-area ?h.white XYZ-area.asc
However I am
-
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Sorry all. Just a test e-mail.
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addressed. If you
Hi all,
I am trying to extract vertexwise surface area values in an ascii files. For
that I am doing
mri_surf2surf
--hemi ?h --srcsubject subject dir area --src_type curv
--trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv
mris_convert -c XYZ-area ?h.white XYZ-area.asc
However I am
Hello all,
I’m using mri_surf2surf to try to resample a subject to fsaverage, so far I
have
mri_surf2surf --hemi lh --srcsubject [SUBJECT] --cortex --trgsubject fsaverage
however I’m pretty certain that I need both —sval and —trgfmt, but this is the
confusing bit as I’m not sure what I
I’m trying to find a way to extract thickness values at each vertex for a given
subject, and as a part of that process I need to ensure that each subject has
been mapped to a common area, such that their vertices have a direct
correspondence, but I’m not entirely sure how to go about it.
I’ve
I am wondering if there a way to account for repeated measures when running a
QDEC analysis. I have 60 scans taken from 39 subjects (ranging between 1 scan
per subject to 5 scans per subject).
Over all I am trying to corrlelate freesurfer measures of thickness and volume
with scores from a
if it's just for visualization you ca use -i, but in general we just
project and unfold on the sphere (and don't use -i which inflates and
drives the surface to the sphere)
On Sat, 12 Apr 2014, Xuelong Zhao wrote:
I attempted the run again using
mris_sphere -w 1 -scale 1 lh.inflated
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