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Curtis Rueden
@ctrueden

It looks like you need to write:

import nibabel as nib
img = nib.load(filename)
data = img.get_fdata()

and then type(data) will be numpy.ndarray instead of Nifti1Image. And you can compute stuff on the data. Does that help?

E | M
@ewuramaminka
ok i just tried
i still got this 'AttributeError: 'Nifti1Image' object has no attribute 'get_fdata'
Curtis Rueden
@ctrueden
Which version of nibabel?
We can check the source code.
From the changelog: it looks like the get_fdata was added in version 2.2? Are you using an older version? If so, try upgrading.
Gotta run to a meeting. Good luck.
E | M
@ewuramaminka
2.0.2
nibabel ver - 2.0.2
Curtis Rueden
@ctrueden
See if you can update to 2.2 or newer.
E | M
@ewuramaminka
I finally got stik to load it
Thanks very much
Dr .Muhammad Anjum Iqbal
@DrMuhammadAnju1_twitter
Hi i DO NOT KNOW , it is proper platform about my problem ! but if any body knows . please let me know . my question is "to get R in python for window "
Mark Harfouche
@hmaarrfk
Mixing languages is hard.

Hi everyone; we're going to try something new for the chat forum. Please direct your browsers to:

https://skimage.zulipchat.com

(or download the app)

We'll try this forum for a few weeks to see how it goes!

E | M
@ewuramaminka

I have dicom files to auto segment using atlas and CNN approach. I’m looking to measure correspondence between these automatic contours and manual contours created by experts. Kindly advise what techniques are best

-Hausdoff distance
-structural similarity index (SSIM)
-Bidirectional local distance measurement (BLD)
-Mean square errors (MSE)
-Dice similarity coefficient
-Distance transforms

Please advise if there are any I haven’t listed and which ones are best for the operation I want to carry out.

Vishesh Mangla
@Teut2711
someone here?
E | M
@ewuramaminka
im wondering.. nobody replied to my question
Josh Moore
@joshmoore
Perhaps try on https://forum.image.sc ?
Kira Evans
@kne42
the scikit-image devs have switched to using zulip and no longer monitor this channel
tonyVeco
@tonyVeco
Hi everyone!!
Mark Harfouche
@hmaarrfk

Hi everyone; we're going to try something new for the chat forum. Please direct your browsers to:

https://skimage.zulipchat.com

(or download the app)

We'll try this forum for a few weeks to see how it goes!

tonyVeco
@tonyVeco
ok, so I could submit my question there ;)
Andrew Schaub
@drewschaub
Http://scikit-image.org/docs/0.7.0/api/skimage.feature.peak.htm goes to wrong url if banner is clicked, scikits-image.org. I know its an older version, but i also noticed the banner is edited to say scikits-image and not scikit
Mark Harfouche
@hmaarrfk
Hi Andrew, Thanks can you please raise an issue on the repo?
Not to ignore your message, but I want this zulip chat message to be the first one people see
Hi everyone; we're going to try something new for the chat forum. Please direct your browsers to:
https://skimage.zulipchat.com
(or download the app)
We'll try this forum for a few weeks to see how it goes!
Andrew Schaub
@drewschaub
will do! Ill switch to the other chatroom as well.
Mark Harfouche
@hmaarrfk
Hi everyone; we're going to try something new for the chat forum. Please direct your browsers to:
https://skimage.zulipchat.com
(or download the app)
We'll try this forum for a few weeks to see how it goes!
Andrew Chalmers
@chalmersgit
Looking at the SSIM metric, does anyone know much about its parameters? Specifically, I've seen that the default window size = 11 is recommended. But to me, this seems like this variable should be dependent on the resolution of the image. Anyone have any thoughts on this?
Andrew Chalmers
@chalmersgit
Just looking at the original ssim paper, they use ~768x512 resolution images. My intuition is to use this as a way of scaling the window size. That is, using the target resolution against the 768x512 as a ratio to scale the window size lower or higher resolution images appropriately.
Andrew Chalmers
@chalmersgit
Oh i see that you are trying to use zulipchat, ill check it out
winash12
@winash12
Hello I had a very basic question here and please feel to guide me to the appropriate link
http://tropic.ssec.wisc.edu/real-time/indian/winds/wm5conv.GIF i have this satellite image. i need to get the latitude and longitude of the contours in that image and convert that into a KML file so that i can load it on google earth. Is that possible with scikit-image ?
Curtis Rueden
@ctrueden
@winash12 Ask on https://skimage.zulipchat.com please!
Joan Massich
@massich
Did I miss read something in doc here, or those two should be giving the same output?
from matplotlib import pyplot as plt
from skimage.draw import disk

fig, axes = plt.subplots(1, 2)
for ax, shape in zip(axes, [None, (10, 10)]):
    img = np.zeros((10, 10), dtype=np.uint8)
    rr, cc = disk((1, 1), 5, shape=shape)
    img[rr, cc] = 1
    ax.imshow(img)
image.png
It is like if one is using a circular buffer and the other one not
Joan Massich
@massich
I mean I don't understand why None gives the full disk and (10,10) does not.
why whouldn't (8,8) give me a partial part of it?
Curtis Rueden
@ctrueden
@massich The scikit-image chat moved from here to https://skimage.zulipchat.com.
Joan Massich
@massich
thx
Salman Abdulla
@salman_python_twitter

from skimage.color.adapt_rgb import adapt_rgb, each_channel, hsv_value
from skimage import filters
from skimage import io
import matplotlib.pyplot as plt
from skimage.color import rgb2gray

image = io.imread('C:/Users/DELL/Desktop/hopfield/monaliza.jpg')

try_to_apply_sobel = filters.sobel(image)
plt.imshow(try_to_apply_sobel)

ValueError: The parameter image must be a 2-dimensional array
how improve this error
Curtis Rueden
@ctrueden
@salman_python_twitter Are you asking how to make the sobel filter work? You can slice the image into 2D. It's might be 3D because it's a JPEG and has distinct red, green, and blue values? You can check with image.shape. Or are you suggesting that the error message be made more clear? I encourage you to join the official chatroom at https://skimage.zulipchat.com to propose something, if so.
Salman Abdulla
@salman_python_twitter
i thinking problem by skimage version