Hi,
One option is to open the volume in 3D Slicer and save it in .mgz format. 3D
Slicer is free to download.
John
On 2013-08-22, at 4:30 PM, Otto Muzik wrote:
>
> Hi,
>
> I am trying to convert a SIEMENS T1-weighted volume to the mgz
> format (via mri_convert) but I am getting constantly
Hello,
I have successfully developed an automated algorithm combining pixel
intensity-based and shape based approaches to segment the lateral ventricles. I
have applied my algorithm to a small data set of 1.5 T1 ADNI images consisting
of 24 AD (subjects with Alzheimer Disease) 19 MCI (subjects
eed sometimes 1mm data cannot resolve the connections. So
> sometimes the temporal or occipital horn are disconnected, and sometimes not.
>
> cheers
> Bruce
>
>
> On Tue, 17 Jul 2012, John Drozd wrote:
>
>> Hello,
>>
>> I have successfully developed an
data but I'm not sure we are allowed to
> distribute it. If you check with them about it and let us know we'll give you
> what we have.
>
> cheers
> Bruce
>
>
> On Tue, 17 Jul 2012, John Drozd wrote:
>
>> Hi Bruce,
>>
>> I apologize for my detailis
Hello,
My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
I noticed that the aparc+aseg.mgz label map is resampled to 1mm x 1mm
x 1mm voxels,
eventhough the .mgz grayscale mri image file remains as per the
original voxel size and is not 1x1x1. mri_convert .nii to .mgz
tra
ate a file with a different
> name. That way you won't have to worry about mixing version.
> doug
>
>
> On 11/30/2012 03:00 PM, John Drozd wrote:
>> Hello,
>>
>> My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
>>
>> I notic
Hello,
I would like to download and install the software described at
http://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping
Your email address is listed on this website.
I cannot find a download link.
We would like to use this with Freesurfer.
Do you know where I can download this softwa
k:
> After sourcing Freesurfer type
>
> which grad_unwarp
>
> HTH
> Dan
>
> On Thu, Dec 20, 2012 at 9:42 AM, John Drozd wrote:
>> Hello,
>>
>> I would like to download and install the software described at
>>
>> http://surfer.nmr.mgh.harvard.edu/fs
Hello,
I am writing a paper for publication in Neuroimage.
I used Freesurfer 4.3 to segment brain anatomy. Lateral ventricles were my
focus.
Can someone please tell me what is the correct way to cite Freesurfer in a
bibliography?
Is there a paper I can cite?
Thank you,
John Drozd
John Jan
>> Can someone please tell me what is the correct way to cite Freesurfer in a
>> bibliography?
>> Is there a paper I can cite?
>>
>> Thank you,
>> John Drozd
>>
>> John Jan Drozd, M.Sc., Ph.D.
>>
>> Financial Secretary
>> Knights
; Reslicing using trilinear interpolation
> MRIresample(): source matrix has zero determinant; matrix is:
> -0.000 -0.000 -0.000 0.000;
> -0.000 -0.939 -0.000 0.000;
> -0.939 0.000 0.000 0.000;
> 0.000 0.000 0.000 1.000;
>
> Do you know why I get this error?
> MRIresample(): source matrix has zero determinant; matrix is:
> -0.000 -0.000 -0.000 0.000;
> -0.000 -0.939 -0.000 0.000;
> -0.939 0.000 0.000 0.000;
> 0.000 0.000 0.000 1.000;
>
> Any help would be appreciated.
>
> John Drozd
> PostDoctorate Fellow
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
lates the total intracranial volume and
ventricle volume?
Also, please let me know if the source code is available for my viewing if
at all possible,
which would be really handy.
Thank you,
John Drozd
PostDoctoral Fellow
Robarts Research Institute,
Imaging Department,
The University of Western On
Hello again,
I incorrectly used the term intercranial volume in my email below.
I meant to type intracranial volume.
john
On Fri, May 15, 2009 at 7:29 AM, John Drozd wrote:
> Hello Bruce and Nick,
>
> Thank you, Bruce, for the clarification that FreeSurfer when reading
> my dic
iated filings."
Does the statement "**Software used for clinical purposes may require
regulatory documentation and associated filings." mean that a version of
FreeSurfer can be used for clinical work?
Thank you for your time,
john drozd
*
__
Hello,
Do you know of any regulations about using FreeSurfer outside of the U.S.,
specifically in Canada?
Thank you,
john drozd
2009/5/25 Pedro Paulo de Magalhães Oliveira Junior
> Software used for clinical purposes need a FDA approval in US.
> FreeSurfer main target is research. If y
Hello,
I am running the reconall steps individually for a firts try.
I noticed that I get a segmentation fault when I run mris_anatomical_stats
as whown below:
[jdr...@trumpet mri]$ mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats
-b -a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab
time.
john drozd
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-cf ../label/aparc.annot.ctab convertedfile lh
3) the error message generated:
Segmentation fault
4) optionally include the subject's /script/recon-all.log
On Tue, May 26, 2009 at 2:23 PM, John Drozd wrote:
> Hello,
>
> I am running the reconall steps individually f
d CSF (I assume
> it did).
>
> doug
>
> John Drozd wrote:
>
>> Hello,
>>
>> I have a question about the eTIV intracranial volume calculation.
>>
>> My question is:
>>
>> Does the eTIV intracranial volume include everything interior to the outer
>
ybe I
should at this stage).
I am just running the commands for a first try.
Thanks,
john
On Tue, May 26, 2009 at 3:13 PM, Douglas N Greve
wrote:
> Can you verify that the disk it is writing to is not full?
>
> Is this an average subject?
>
> doug
>
> John Drozd wrote:
>
&
a first try.
>>
>> Thanks,
>> john
>>
>> On Tue, May 26, 2009 at 3:13 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>Can you verify that the disk it is writing to is not full?
>&g
the file
> and directory?
>
> John Drozd wrote:
>
>> Hi Doug,
>>
>> It is writing to the trumpet directory which is not full.
>> It does write out the output file aparc.annot.ctab, but seg faults at the
>> end.
>>
>> Here is the df -h output fo
ster program to
FreeSurfer called Neuroquant is from FreeSurfer?
Other than Neuroquant being able to be used clinically, I was wondering if
the functionality is different.
Thank you for your time,
John Drozd
Postdoctoral Fellow
Robarts Research Institute
Medical Imaging Department
The University of Western
LinkedIn
Freesurfer,
I'd like to add you to my professional network on LinkedIn.
- John
Confirm that you know John Drozd
https://www.linkedin.com/e/isd/1058664165/nSlXVFJx/
--
(c) 2010, LinkedIn Corporation___
Frees
this dicom series?
Thank you,
John
--
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
ll try these tools out as well.
Thank you for your time,
John
On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl wrote:
> recon-all \
>-i \
>-s \
>-sd \
>-all
>
>
> cheers
> Bruce
>
>
>
> On Tue, 5 Jul 2011, John Drozd wrote:
>
> sorry, but the majority of the time is required. We're working to speed
> things up, but it is complicated software with multiple nonlinear warps,
> segmentation procedures, etc
>
>
> Bruce
>
>
>
> On Tue, 5 Jul 2011, John Drozd wrote:
>
> Hi Bruce an
> which is what we usually do. Or you can use cuss
>
>
>
> On Jul 5, 2011, at 5:11 PM, John Drozd wrote:
>
> Hi Bruce,
>
> Okay, thank you. I understand and can see that to do an accurate job, the
> pipeline must be complicated.
> I have eight processors on my linux
28 matches
Mail list logo
