Hi,
>From https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
"SubCortGray - includes thalamus, caudate, hippocampus, amygdala, accumbens,
ventral DC, substancia nigra (if there). This is a simple voxel count of
structures identified as subcortical GM."
Could you please let me know if
Thanks for your help. Yes.
It looks like it is crashing during make_roi_paths.m
Any ideas? Thanks.
On Fri, 30 Sep 2016 06:32:06 -0700 Alan Francis
alandarkene...@gmail.com wrote
Hi Prasser:
Did you set the environment for MATLAB e.g.,
setenv MATLABPATH /Applications
Hi, Reposting. Thanks.
On Tue, 27 Sep 2016 16:53:21 -0700 prasserpras...@zoho.com wrote
Hi,
I'm looking to please get some help with -lgi.
I'm using matlab R2015b and FS5.3 with
recon-all -s subj_id -lgi
on os x 10.11.
Looking at the output, the first error occurs about here:
Hi,
When using mri_convert to create 001.mgz from dicom that have *not* been
anonymized does any patient, institution, study description etc information get
transferred into the 001.mgz?
Thanks.
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Hi,
I'm looking to please get some help with -lgi.
I'm using matlab R2015b and FS5.3 with
recon-all -s subj_id -lgi
on os x 10.11.
Looking at the output, the first error occurs about here:
preparing pial mesh structure ...
...searching for mesh edges...done (206.94 sec).
... creating path
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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Hi,
On the download page it mentions that Freesurfer v5.3 is not compatible with OS
X 10.11 because of an implementation of SIP. As a test, I have run a few
subjects with v5.3 under OS X 10.11.3 with SIP enabled but was unable to see
any problems, with all test subjects completing without
Hi,
I was hoping to get confirmation on the set of command below to display the
mean rate of
change of thickness on fsaverage from a group of subjects in a longitudinal
study. Please let me know if I'm missing anything?
Thanks,
P
mris_preproc --fsgd group.fsgd \
--cache-in
Hi,
If I have a set of subjects from a study collected at time 0 (T0) and a subset
of these subjects that also have data collected at time 1 (T1), can I run qdec
on the T0 subject's with no T1 together with the longs of the subject's at T0
that have a T1?
Thanks,
P
Hi,
For memprage data collected on a 3T scanner could you please let me know what
nu_correct flag should be used for recon-all? Should we use -nuintensitycor-3T?
Thanks,
P
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Hi,
On this page https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it
mentions it is recommended to check if all CPs are accurately placed in the
long.
I was wondering what is the best way to do this?
I know I can type in the RAS coordinates from the control.dat file and check
Hi,
If I am only interested in the gm thickness (ThickAvg) of a specific
structure/s (e.g. precentral) is it sufficient to only QC these specific
structures/s or does the wm and pial surface need to be accurate across the
entire hemisphere for the accurate determination of gm thickness of
used for the -surfsegedit.
Looking forward to a reply, thanks,
P
On Mon, 18 May 2015 16:27:31 -0700 prasser lt;pras...@zoho.comgt; wrote
Hi,
This is a repost, hope someone can please comment?
Thanks.
On Wed, 06 May 2015 00:07:17 -0700 prasser lt;pras...@zoho.comgt
Hi,
This is a repost, hope someone can please comment?
Thanks.
On Wed, 06 May 2015 00:07:17 -0700 prasser lt;pras...@zoho.comgt; wrote
Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after
-surfsegedit is that, new surfaces are created during -autorecon2
the -long …. stuff
Martin
On Apr 28, 2015, at 12:46 AM, prasser lt;pras...@zoho.comgt; 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 -surfsegedit
we need to re-run
recon-all
=
but= it= looks= right= to= me= (except= typo= in= what=
should= be= -autorecon3).= second= one= i= think= you=
want= rerun= mri_segstats= and= mris_anatomical_stats= commands,=
which= done= by= autorecon3=
cheers
Bruce
On Mon, 20 Apr 2015, prasser wrote:
Dear All,
I wanted
=
should= be= -autorecon3).= second= one= i= think= you=
want= rerun= mri_segstats= and= mris_anatomical_stats= commands,=
which= done= by= autorecon3=
cheers
Bruce
On Mon, 20 Apr 2015, prasser wrote:
Dear All,
I wanted to check that corrections to a Long pial surface through edits
be done
by autorecon3
cheers
Bruce
On Mon, 20 Apr 2015, prasser wrote:
Dear All,
I wanted to check that corrections to a Long pial surface through edits
to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the
command:
recon-all -long tpN1 templateID -autorecon2
and mris_anatomical_stats commands, which should be done
by autorecon3
cheers
Bruce
On Mon, 20 Apr 2015, prasser wrote:
Dear All,
I wanted to check that corrections to a Long pial surface through edits
to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the
command:
recon-all -long
Dear All,
I wanted to check that corrections to a Long pial surface through edits to
brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command:
recon-all -long tpN1 templateID -autorecon2-pial -autorecom3
Is this correct?
Also, after editing the Long aseg.mgz to correct the
Say, following the set of commands given on the FsTutorial/Diffusion page
(freesurfer.net/fswiki/FsTutorial/Diffusion)
On Mon, 15 Sep 2014 05:26:01 -0700 Bruce Fischl
lt;fis...@nmr.mgh.harvard.edugt; wrote
what kind of DTI analysis?
On Sun, 14 Sep 2014, prasser wrote:
gt; Hi
Hi,
Could you please let me know if it's okay to use subjects analyzed using
Freesurfer 5.1 (os x 10.6) for DTI analysis using Freesurfer 5.3 (os x 10.8)?
Thanks.
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Dear All,
For longitudinal data sets, is there a way that the lh.pial surface from the
Base can be transformed into the brainmask.mgz space of a Cross so that it can
be viewed with tkmedit on the Cross brainmask.mgz?
Thanks,
Paul
___
Freesurfer
Dear All,
For longitudinal data sets, is there a way that the lh.pial surface from the
Base can be transformed into the brainmask.mgz space of a Cross so that
it can be viewed with tkmedit on the Cross brainmask.mgz?
Thanks,
Paul
___
Freesurfer
/freeview
doug
On 04/28/2014 11:53 PM, prasser wrote:
gt;
gt; Thanks.
gt;
gt; Using:
gt;
gt; mri_convert dicom output.nii -iid 0 -1 0 -ijd 0 0 -1 -ikd -1 0 0
gt;
gt;
gt; Seems to do the trick.
gt;
gt; I have attached a figure with the left image from mri_convert and the
gt; right
Hi,
I am still having some concerns using mri_convert on Skyra volumes that I'm
hoping can please be addressed.
On this occasion I have used mri_convert to convert a single dicom file to
nifti from a volume collected on a siemens Skyra scanner using Freesurfer5.3 on
CentOS5.7.
When viewing
was acquired in. If you want to upload the dataset we can take a look and
confirm
cheers
Bruce
On Sun, 27 Apr 2014, prasser wrote:
gt; Hi,
gt;
gt; I am still having some concerns using mri_convert on Skyra volumes that
I'm
gt; hoping can please be addressed.
gt;
gt
Hi,
I am still having some concerns using mri_convert on Skyra volumes that I'm
hoping can please be addressed.
On this occasion I have used mri_convert to convert a single dicom file to
nifti from a volume collected on a siemens Skyra scanner using Freesurfer5.3 on
CentOS5.7.
When viewing
orientation using the flag
--out_orientation followed by LIA (for example). Maybe the input file needs
to be in a specific orientation before it can be converted properly.
On Wed, Dec 4, 2013 at 9:56 PM, prasser lt;pras...@zoho.comgt; wrote:
Hi,
I'm currently having problems converting
Hi,
I'm currently having problems converting .IMA files collected from a Siemens
Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x.
Using:
mri_convert -it siemens -ot mgz 1.IMA test.mgz
I get the error message:
does not contain a Siemens ASCII header has this file been
The flag -autorecon2-noaseg seems to no longer be used in version 5.1.
i.e. ERROR: Flag -autorecon2-noaseg unrecognized.
For edits made to aseg.mgz, could you please let me know what recon-all flags
are recommended for version 5.1 for the case described in the email
Hi,
I was wondering if there is any documentation on mri_cnr, particularly how the
noise is calculated.
Thank you,
Paul
gt;
gt; thanks Dr. B.that helped a lot
gt;
gt; - Original Message -
gt; From: Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt;
gt; To: Kushal
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