Ok I try this out using MATLAB.
Thanks Bruce,
On Wed, Dec 17, 2014 at 7:32 PM, Bruce Fischl
wrote:
>
> Hi Gunjan
>
> I can't help you preserve it in minc and using someone else's tools to
> convert slices to nifti. Can you work in matlb instead? If so, you can
> convert the minc to .mgz with mri
Hi Gunjan
I can't help you preserve it in minc and using someone else's tools to
convert slices to nifti. Can you work in matlb instead? If so, you can
convert the minc to .mgz with mri_convert, then load the mgz into matlab
using either MRIread or load_mgh (which will both return the directi
Hi Bruce,
I am sorry that you could not get me properly.
My query is, how can I preserve direction cosine information. As I am new
to this issue, any help would really be appreciated.
Thanks,
Gunjan
On Wed, Dec 17, 2014 at 7:08 PM, Bruce Fischl
wrote:
>
> Hi Gunjan
>
> our coordinate systems ar
Hi Gunjan
our coordinate systems are extensively documented here:
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt
cheers
Bruce
On
Wed, 17 Dec 2014,
Gunjan Gautam wrote:
Hi Bruce,
I can view the file using "freeview -v file.mnc"
Hi Bruce,
I can view the file using "*freeview -v file.mnc*" but I think that won't
solve my problem as I need to switch from 2D to 3D and vice versa.
I will be thankful if you could be a bit specific about "preserving the
direction cosine information" as I am facing difficulty to process these
vo
Thank you Bruce,
I try this out.
On Dec 16, 2014 7:58 AM, "Bruce Fischl" wrote:
> I'm not sure what to tell you then. You need to save it in a format that
> preserves the direction cosine information. This shouldn't be that hard to
> do (e.g in matlab)
> Bruce
>
>
> On Tue, 16 Dec 2014, Gunjan G
I'm not sure what to tell you then. You need to save it in a format that
preserves the direction cosine information. This shouldn't be that hard to
do (e.g in matlab)
Bruce
On Tue, 16 Dec 2014, Gunjan
Gautam wrote:
I think that won't resolve my issue because I need to deal with a specific
I think that won't resolve my issue because I need to deal with a specific
set of noise removal algorithms and nonuniformity correction algorithms.
On Dec 16, 2014 7:50 AM, "Bruce Fischl" wrote:
> have you tried just giving the original volume to recon-all? We typically
> deal with this kind of t
have you tried just giving the original volume to recon-all? We typically
deal with this kind of thing internally (and in 3D, not on a
slice-by-slice basis)
cheers
Bruce
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
Sure,
My data(3D volume) is having different ranges of noise and nonuniformity
Sure,
My data(3D volume) is having different ranges of noise and nonuniformity so
I want to apply different algorithms to get rid of these and analyze the
extent.
On Dec 16, 2014 7:40 AM, "Bruce Fischl" wrote:
> Hi Gunjan
> can you elaborate? What kind of modifications would you want to make to
Hi Gunjan
can you elaborate? What kind of modifications would you want to make to
each slice?
Bruce
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
Yes Bruce, minc is a volume but I want to perform some experiments and see
the aftereffects.
This is how I come from 3D to 2D to make changes in each
Yes Bruce, minc is a volume but I want to perform some experiments and see
the aftereffects.
This is how I come from 3D to 2D to make changes in each slice and again I
rejoin these slices (2D to 3D). I don't know if anything other than NIfTi
gives this much flexibility or it could be dealt without
isn't the minc a volume? It certainly supports holding an entire volume
in a single file
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
Ok , I try this out.
I converted it to nii because after processing 2D slices of the volume, I
can easily switch to 3D space(ie stacking) in order to apply brain
Ok , I try this out.
I converted it to nii because after processing 2D slices of the volume, I
can easily switch to 3D space(ie stacking) in order to apply brain
extraction tools as NIfTi provides some of the useful utilities.
On Dec 16, 2014 6:59 AM, "Bruce Fischl" wrote:
> why do you need to c
p.s and make sure that the anatomical directions that freeview shows
reflect the actual orientation of the brain
On Tue, 16 Dec 2014, Gunjan
Gautam wrote:
Hi Bruce,
Originally, data was in MINC format.
On Dec 16, 2014 1:54 AM, "Bruce Fischl" wrote:
Hi Gunjan
what was the origi
why do you need to convert it to nifti? Can you process the minc directly?
See if freeview can display it:
freeview -v file.mnc
On
Tue, 16 Dec 2014, Gunjan Gautam wrote:
Hi Bruce,
Originally, data was in MINC format.
On Dec 16, 2014 1:54 AM, "Bruce Fischl" wrote:
Hi Gunjan
Hi Bruce,
Originally, data was in MINC format.
On Dec 16, 2014 1:54 AM, "Bruce Fischl" wrote:
> Hi Gunjan
>
> what was the original data format that you had? Once you have converted it
> to nifti in your current stream you can no longer use the data, so you have
> to start further upstream
>
> c
Hi Gunjan
what was the original data format that you had? Once you have converted
it to nifti in your current stream you can no longer use the data, so you
have to start further upstream
cheers
Bruce
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
I don't have dicom for this subject but it can
I don't have dicom for this subject but it can easily be converted to from
.nii to .dcm.
I try this out and get back to you if I stuck at some point.
Thanks,
Gunjan
On Dec 16, 2014 12:49 AM, "Bruce Fischl"
wrote:
> do you have the dicom data for this subject? If so, it will be separated
> into
do you have the dicom data for this subject? If so, it will be separated
into different "series" each corresponding to one acquisition (e.g. a
T1-weighted one such as mprage or FLASH). Typically that series will have
more than 150 slices (since that's what it takes to cover the brain at
close t
Hi Bruce,
I am sorry to say that I did not get you properly.
Could you please say a bit more about "a *single* slice in the correct
series ". I want to try this option.
On Dec 16, 2014 12:13 AM, "Bruce Fischl" wrote:
> Hi Gunjan
>
> freesurfer will handle the dicom slices just find. Just give r
Hi Gunjan
freesurfer will handle the dicom slices just find. Just give recon-all a
*single* slice in the correct series with the -i command and it should
work. I don't know medcon, but it is not propagating the direction cosine
info into the nifti, which means that the nifti files are effectiv
Thanks Bruce,
I used "medcon" command (Ubuntu) for the stacking of 2D slices in order to
convert it in a volume. These slices were obtained from a volume itself and
after making some intensity changes, a volume is formed (using medcon)
again. Then I fed this volume as input to FS in order to extra
Hi Gunjan
the problem is that the nifti volume doesn't contain the direction cosine
information that we need to figure out what directions are A/P, I/S and
L/R. mri_convert warns of this:
mri_convert m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-1.nii.gz test.mgz
mri_convert m000-stacks-m00
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