l if you explain how does it interpret from matrix.
>
> Thanks,
> Ritesh Mahajan
>
> - Original Message -
> From: "Greve, Douglas N.,Ph.D."
> To: "freesurfer"
> Sent: Friday, January 25, 2019 10:26:47 PM
> Subject: Re: [Freesurfer] Orientation by
d be really helpful if you explain how does it interpret from matrix.
Thanks,
Ritesh Mahajan
- Original Message -
From: "Greve, Douglas N.,Ph.D."
To: "freesurfer"
Sent: Friday, January 25, 2019 10:26:47 PM
Subject: Re: [Freesurfer] Orientation by direction cosines
mri_in
January 25, 2019 10:26:47 PM
Subject: Re: [Freesurfer] Orientation by direction cosines
mri_info will do it. If you just want the orientation string, you can
add --orientation. Or do you still want the interpretation of the matrix?
On 1/25/19 10:10 AM, Bruce Fischl wrote:
> Hi Ritesh
>
&g
mri_info will do it. If you just want the orientation string, you can
add --orientation. Or do you still want the interpretation of the matrix?
On 1/25/19 10:10 AM, Bruce Fischl wrote:
> Hi Ritesh
>
> I think that mri_info will try to figure this out and tell you (in the
> "Orientation" output).
Hi Ritesh
I think that mri_info will try to figure this out and tell you (in the
"Orientation" output).
cheers
Bruce
On Fri, 25 Jan 2019, Ritesh Mahajan wrote:
>External Email - Use Caution
>
> Hello Team,
>
> Can any one please explain how we come to know whether it is RAI or RAS or
External Email - Use Caution
Hello Team,
Can any one please explain how we come to know whether it is RAI or RAS or any
other orientation through direction cosines:
Below is the direction cosine: I saw some non zero and negative values in non
diagonal values of matrix. What d
Dear Zhewei,
I think that the problem you report is caused by the fact, that .mat file from
FLIRT codes vox2vox transformation, so that cannot be applied to another
dataset (in your case fMRI) unless it has the same geometry as the original
image the .mat file was generated on.
Antonin
Can
Can you send your freeview command line and pictures of the mismatch?
On 2/9/17 5:58 PM, Zhewei Wang wrote:
Hi all,
I have a problem maybe relevant to the orientation of images in
freeview. I have two images, one is fMRI and one is MRI. They are
produced from the same machine at the same ti
Hi all,
I have a problem maybe relevant to the orientation of images in freeview. I
have two images, one is fMRI and one is MRI. They are produced from the
same machine at the same time. I loaded both of them in freeview and it
showed they are matched very well, even they have different resolution
Hi Daniel
do you mean the white and pial surfaces? You can certainly compute the
surface normals for them, or use mris_convert to do it:
mris_convert -n lh.white lh.white.normals.asc
will compute and write out the surface normals (using an outwards-pointing
convention) for the white surface t
Hi Bruce,
That was very quick! Yes, I do believe this is what I am looking for. Thank
you so much!
Best
Daniel
On Fri, Nov 13, 2015 at 4:53 PM, Bruce Fischl
wrote:
> Hi Daniel
>
> do you mean the white and pial surfaces? You can certainly compute the
> surface normals for them, or use mris_con
Hi,
I am looking for a way of figuring out the orientation vector of the
neurons within a voxel. That is, in which direction is the dipole of the
neurons pointing at. This could be possible to calculate if there is a way
of determining the position of the inner and outer layer for each voxel,
whic
Hi Stefani
are the axes also flipped if you view in freeview?
cheers
Bruce
On Thu, 11 Jun 2015,
Stefani O'Donoghue wrote:
Hi Freesurfer, We've carried out the mri_label2vol step for ROIs in one
hemisphere. When opening in ITKsnap the orientations appeared flipped, with
the axial ROIs overlay
Hi Freesurfer,
We've carried out the mri_label2vol step for ROIs in one hemisphere. When
opening in ITKsnap the orientations appeared flipped, with the axial ROIs
overlayed onto the coronal orientation, and coronal over the axial, and the
sagittal plane appeared rotated.
Can anyone help us fix thi
try setting the orientation string to LIA
On 08/19/2013 11:15 AM, Mark Plantz wrote:
> Hello freesurfers,
>
>I have an image that is in RAS orientation with the axial primary
> slice direction. Is there anyway to change this to LIA orientation
> with the coronal primary slice direction? I am
Hello freesurfers,
I have an image that is in RAS orientation with the axial primary slice
direction. Is there anyway to change this to LIA orientation with the
coronal primary slice direction? I am assuming mri_convert would work, but
I'm not sure which flags to use.
Thanks in advance.
MP
__
what format is your input data in?
On Mon, 3 May 2010, Ilana Hairston wrote:
> I have also been getting error messages, after Talairach correction using
> tkregister2
>
> *...@# Talairach Failure Detection Mon May 3 09:57:40 EDT 2010
> /usr/local/freesurfer/subjects/FS060828cr/mri
>
> talairach_a
I have also been getting error messages, after Talairach correction using
tkregister2
*...@# Talairach Failure Detection Mon May 3 09:57:40 EDT 2010
/usr/local/freesurfer/subjects/FS060828cr/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms
Hi Jan,
what was your input data?
Bruce
On Mon, 3 May 2010, Janani Dhinakaran wrote:
> Hello experts,
>
> I've been having some trouble with the talairach during recon. I followed
> previous instructions and checked the rawavg image and found that it was in
> wrongly oriented.
> The sagittal pic
Hello experts,
I've been having some trouble with the talairach during recon. I followed
previous instructions and checked the rawavg image and found that it was in
wrongly oriented.
The sagittal picture was appearing under coronal but upsidedown, the coronal
picture was sideways in the transverse
How do you know? It should be in the same space.
Bruce
On Jan 21, 2010, at 5:01 PM, yzha...@artsci.wustl.edu wrote:
> I have run the following command to create a 001.mgz file from raw
> *.dcm
> data:
>
> recon-all -s -i
>
> The output 001.mgz file is not in the same native space as the
>
It should be in the same space. How do you know it is not? Make sure
that you just pass one dicom file to recon-call (I noticed that you
have a wildcard character in there).
doug
yzha...@artsci.wustl.edu wrote:
> I have run the following command to create a 001.mgz file from raw *.dcm
> data
I have run the following command to create a 001.mgz file from raw *.dcm
data:
recon-all -s -i
The output 001.mgz file is not in the same native space as the original
*.dcm data. Could anyone tell me what space the 001.mgz file is in? Does
the above command change the orientation (i.e does it r
du]
> Sent: Monday, 2 November 2009 11:20 PM
> To: Dominic Brendon Dwyer
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] orientation problem resulting in talairach
> failure
>
> Hi Dominic,
>
> do you have access to any format previous to the analyze one? It doe
m: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Monday, 2 November 2009 11:20 PM
To: Dominic Brendon Dwyer
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] orientation problem resulting in talairach
failure
Hi Dominic,
do you have access to any format previous to the
Hi Dominic,
do you have access to any format previous to the analyze one? It doesn't
preserve orientation info, and all bets are off once you go through it.
cheers
Bruce
On
Mon, 2 Nov 2009, Dominic Brendon Dwyer wrote:
> Dear Freesurfer developers,
>
>
>
> I have a few analyse images which are
Dear Freesurfer developers,
I have a few analyse images which are oriented incorrectly that are part
of a larger dataset. When viewed in tkmedit, what is supposed to be
coronal is actually displayed as axial and the sagittal is flipped. In
these cases the Talairach transform fails spectacularl
That is probably just the way they are oriented in the nii file. BTW,
why are you using bshort? I'm trying to push people into using nii.
doug
Leila Reddy wrote:
Hi,
I am trying to convert SPM5 .nii files into bshort and I used the
following command:
mri_concat fkoch-0007*.nii --o bol
Hi,
I am trying to convert SPM5 .nii files into bshort and I used the following
command:
mri_concat fkoch-0007*.nii --o bold/007/fspm_000.bshort
The command seems to work in that I have a bunch of bshort files in my bold/007
directory but when I try to view the slices (using sliceview-sess fo
You can try using the --in_orientation in mri_convert (see help). You
can try various strings until it looks right in tkmedit. Though, as
Bruce points out, you still won't know whether you got left and right
correct.
doug
On Wed, 24 Oct 2007, Nurunisa Neyzi wrote:
Hi, I have these analyze
Hi Nurunisa,
is analyze all you have? How do you know left from right? MRIreorder
probably wants an isotropic volume with the same image dimensions in the
different directions. You can try "conforming" it first and see if the
reordering works then. I would be *very* careful about left/right sw
Hi, I have these analyze files with wrong orientation
I can change their orientation using fslswapdim
but when I convert them to mgz files using mri_convert, the orientation is
wrong again.
i tried the following
reading from 001.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, 0, -1)
j
Is the orig.mgz oriented correctly? How about the rawavg.mgz and the
orig/001.mgz?
Dick, Rachel wrote:
Hello all,
I have been using
Freesurfer for quite some time. However,
I have run into a problem. I am using a properly oriented input image
(just
like all others I
what is the input data? The most reliable thing is to use the dicoms as
inputs.
Bruce
On Fri, 27 Jul 2007, Dick, Rachel wrote:
Hello all,
I have been using Freesurfer for quite some time. However, I have run
into a problem. I am using a properly oriented input image (just like
all others
Hello all,
I have been using Freesurfer for quite some time. However, I have run
into a problem. I am using a properly oriented input image (just like
all others I have used before), but when I go to look at the
brainmask.mgz after autorecon1, the image is flipped on the y axis. I
have used
Can you give us more details on exactly what you're doing? Are you reading
the dicoms directly? Converting them first? Viewing them with tkmedit?
On Wed, 26 Apr 2006, adam walczak wrote:
Hello,
Our scanner outputs data so that the different orientations (sagittal, coronal) are not
actually t
Hello, Our scanner outputs data so that the different orientations (sagittal, coronal) are not actually those orientations. For example: the "sagittal view" from our scanner is seen when using the horizontal view in tkmedit. And the sagittal view button produces the coronal view. How can this b
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