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Hi Freesurfers.
There is a "ctx-lh/rh-corpuscallosum" label in Freesurfer, but the
Corpus Callosum is not considered to be in the cortex. Can you explain
precisely what this label refers to?
Th
. Can you run this
cd /execute/freesurfer2016/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
--i orig.mgz --o orig_nu.mgz
and send the terminal output?
On 6/29/2020 7:01 AM, Ian wrote:
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I have attached the log - is there any
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I have attached the log - is there any chance you could tell me what the
problem is?
Thanks,
Ian
--
Mon Jun 29 10:53:22 UTC 2020
/execute/freesurfer2016
/usr/local/freesurfer/bin/recon-all
-all -subjid ./freesurfer2016
subjid freesurfer2016
setenv
/5.28 /usr/share/perl/5.28
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at
/usr/local/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at
/usr/local/freesurfer/mni/bin/nu_correct line 37.
Could you advise please?
Thanks,
Ian
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ong to the 3rd ventricle.
>
> I hope that is what you were asking?
>
> Tim
>
>> On June 17, 2020 at 11:41 AM Ian Hardingham wrote:
>>
>>
>> External Email - Use Caution
>>
>> Are the ventricles currently in V6 Surf directory as a set of vertices,
>
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Are the ventricles currently in V6 Surf directory as a set of vertices,
or a labelled list of voxels, or anything like that?
Ian
On 16/06/2020 13:39, Ian wrote:
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Hi Freesurfers.
I'm looking to find the center
. Greve wrote:
Yes, I put a linux version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids
On 6/16/2020 10:32 AM, Ian Hardingham wrote:
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Is this only in FSL 7 Doug? I can't find it in 6.
On 16/06/2020 14:59, Douglas N. Greve wrote:
Try
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Thank you so much Doug.
Ian
On 16/06/2020 15:44, Douglas N. Greve wrote:
Yes, I put a linux version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids
On 6/16/2020 10:32 AM, Ian Hardingham wrote:
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Is this only in FSL 7 Doug? I can't find it in 6.
On 16/06/2020 14:59, Douglas N. Greve wrote:
Try mri_segcentroids. Run it with --help to get docs
On 6/16/2020 8:39 AM, Ian wrote:
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Hi Freesurfers.
I'm
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Hi Freesurfers.
I'm looking to find the center of the various Ventricles. Are they
included in the freesurfer segmentation images with a specific code?
If not, what approach would you use?
Thanks,
Ian
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Sorry, found them, never mind!
On 18/05/2020 12:26, Ian wrote:
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Hi freesurfers,
Is it possible to download freesurfer versions 4 and 5?
Thanks,
Ian
--
*Ian Hardingham
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Hi freesurfers,
Is it possible to download freesurfer versions 4 and 5?
Thanks,
Ian
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Thanks Bruce.
On 13/05/2020 15:41, Bruce Fischl wrote:
Hi Ian
we don't register to an individual subject - we register to a
probabilistic atlas compiled from many subjects. The fsaverage
subjects were also generated from that data so
BJECTS_DIR/fsaverage/lh.sphere.reg a registration to? If not, where
can I find the subject that recon-all registers to?
Thanks,
Ian
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,
not average space.
So if I have five subjects - I would like the same number of points for
each one, which I thought I would get by registering the average to each
of them...
On 11/05/2020 18:56, Douglas N. Greve wrote:
Ian, it seems like you want two different things. When you run
mri_surf2surf
not alter the number of
vertices in them. There is no 1-to-1 correspondence between the vertices of the
2 meshes.
May I ask why you need this? What do you want to achieve?
Tim
On May 11, 2020 at 2:11 PM Ian wrote:
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I'm just going to try this again, but
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I'm just going to try this again, but this time with a different command:
mris_apply_reg --src-xyz
/usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg
/home/ian/lh_reg.white --streg
/usr/local/freesurfer/subjects/fsaverage/surf
22:45, Douglas N. Greve wrote:
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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Thanks Doug - yes, I'd like the vertex coordinates in the same format
as the local subject surface files are in.
On 07/05
this mean an affine (12dof) transform? And what information do
you want? An XYZ coordinate?
On 5/7/2020 11:06 AM, Ian Hardingham wrote:
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I'd like to get a set of points to compare across several brains, so
that the nth point in brain A is in roughly the
to positions on the target
brain (which may well not be vertices in the target geometry.)
On 07/05/2020 15:59, Douglas N. Greve wrote:
I don't understand. What is the difference between the target brain
and the target subject's vertices?
On 5/7/2020 2:17 AM, Ian Hardingham wrote
should be the number of vertices in the target subject (and is in the
typical range for an individual subject)
On 5/6/2020 10:21 AM, Ian Hardingham wrote:
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FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while lo
00)
c_(ras) : (-0.5431, 8.9290, -17.0723)
file : /media/ian/bronson/subject/T1_nifti.nii.gz
Volume Geometry vox2ras
-0.99905 -0.04362 0.0 92.25847;
-0.04362 0.99905 0.0 -99.12585;
0.0 0.0 1.0 -145.07230;
0.0 0.0 0.0 1.0;
Volume Geometry v
trgsurfval {output_dir}/registered_lh.white
My newly registered lh.white file is half the size:
3316997 May 6 10:41 /home/ian/cdm_registered_test/registered_lh.white
(and appears to have half the vertices accordingly.)
So this must be incorrect, or at least not my intended purpose.
To try and be
, but the interface might be a
little easier
On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no definitely not "w" format, which we don't use for anything
anymore. YOu should use tval-xyz also I think
On Tue, 5 May 2020, Ian Hardingham wrote:
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It wo
--srcsubject fsaverage --sval-xyz pial
--trgsubject fs_target --trgsurfval ./registered_rh.pial --trg_type w
The white calls output seems to be fine, but the pial ones aren't. I
somewhat naively trued trg_type pial but that wasn't correct.
On 05/05/2020 17:33, Ian Hardingham wrote:
Thanks Bruce
", but if
it's ".pial" it outputs ".pial.w", which I find a little curious.
Ian
On 05/05/2020 16:34, Bruce Fischl wrote:
yes, check out options like:
--sval-xyz
if you need further help though I'll have to defer to Doug :)
Bruce
On Tue, 5 May 2020, Ian Hardingha
:43, Bruce Fischl wrote:
Hi Ian
you can use mri_surf2surf to map surfaces between subjects, but our
atlas isn't really a surface. You can use the surfaces in the
fsaverage dir, but they are meant for visualization and are much
smoother than individuals
cheers
Bruce
On Tue, 5 May 2020, Ian
.
Any helpers on how to achieve this?
Thanks,
Ian
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as the value... or is the volume between the surfaces calculated
somehow?
Thanks,
Ian
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image is based on Ubuntu;
and nothing else is being explicitly run on the instance while recon-all
is running.
Thanks,
Ian
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the logs - the only immediate error I can see is "Cannot
find rh.white.H".
Any advice would be much appreciated, thank you.
Ian
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Chief Technology Officer
signature_873986710
ian.harding...@oxfordbraindiagnostics.com
<mailto:terry.poll...@oxfordbraindiagnostics.
:$PATH
2. I have set FREESURFER_HOME
Attached at the end is some output from both failing and successful runs.
3. nu_correct exists in freesurfer/mni/bin
4. Perl is present and correct on both systems.
Thank you in advance,
Ian
FAILING OUTPUT
as input to see if it provides a better starting
point than whole brain labels. Are there any other inputs we'd need?
Best wishes,
Ian Malone
--
Research Associate
Dementia Research Centre
Queen Square Institute of Neurology
UCL
London WC1N 3BG
Hello,
Is there a way to specify a nonisotropic PSF when using mri_gtmpvc? I have
reason to believe there are differences between the axial and transverse
resolutions of the PET scanner in my study and would like to incorporate
them if possible.
Thanks,
Ian Kennedy
looking for lies elsewhere.
Any help would be highly appreciated!!
ian
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The information in this e-mail is intended only
the support of the UK
Alzheimer's Society and the kind permission of the original study
participants and funders. Full acknowledgements can be found at
https://www.ucl.ac.uk/drc/research/miriad/Acknowledgements.
Best wishes for your future research,
Ian Malone
Dementia Research Centre, UCL
values when nothing is significant?
Thanks,
Ian
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The information in this e-mail is intended only for the person to whom
no intelligible way to make an overlay out of interactions,
unless you look at the F-test output one contrast at a time (e.g.,
what areas show a significant interaction in thickness between
dependents vs abusers and use in the last month?).
Take care,
Ian Carroll
Hi
Thanks guys for the reply, I have fixed this now.
ian
-Original Message-
From: dgw [mailto:dgwake...@gmail.com]
Sent: 07 March 2012 19:55
To: Nick Schmansky
Cc: Ian Charest; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET
and all seems fine.
Any Idea what could be going wrong?
Best Wishes
Ian Charest
==
talairach_avi.log:
/imaging/ic01/subjects/subject01/mri
/imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi
--i orig.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach_avi,v 1.9 2011/03/02 18:38
Hi again
More on this note:
Using the previous stable version 4.3.0 that I have installed here, I have
absolutely no problem in running the same process.
ian
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ian Charest
Sent: 07 March
install is and where your subject directory lies...
alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv
SUBJECTS_DIR ~/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh'
now if you close your terminal and open a new one, freesurfer should work.
Hope it helps
Ian
a register.dat file here or even a
template file, as I want to generate a volume in RAS space, from a label which
I would think is also in RAS space.
As for the template file, should it be orig.mgz?
Any suggestions here would be appreciated!
Regards
Ian Charest
Richard G. Edgar wrote:
On Tue, 2011-04-05 at 11:23 +0200, Knut J Bjuland wrote:
Will a Tesla C2050 or another good CPU be able to reduce the running
time from 20-24 hr to less time like for instance 8hr or below that
time.
On the standard test case we use here, a full recon-all run
On 05/04/11 16:55, Richard G. Edgar wrote:
On Tue, 2011-04-05 at 16:30 +0100, Ian Malone wrote:
Richard G. Edgar wrote:
On the standard test case we use here, a full recon-all run takes 8
hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins when using
the Tesla C2050.
Would I
The file is the right size, however further investigation shows that
vox_offset in the .hdr file was (incorrectly) non-zero; equal to 1, so
mri_convert is correct in skipping one byte at the start. Sorry for the
fuss.
Ian
Douglas N Greve wrote:
Can you verify that the file is the right
ones). Using the 1mm^3 voxel registered
volume as the template does not show this problem, neither does viewing
the label overlaid on orig.mgz in tkmedit. Is there anything I can
adjust to avoid this while still outputting a volume in the original
image dimensions?
Thanks,
Ian Malone
inline
-v4.0.3
Kernel info: Linux 2.6.21.5-smp i686
Thanks,
Ian Malone
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