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<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Hi again ! <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">OK I get a bit more why I can't do that so easily : I extracted the slices of the NIFTI image (“img_sobel_data”), filtered them, but I wasn't change the NIFTI image itself !!!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> img = nib.load(im_path)
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> img_sobel = nib.load(im_path)
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> # Name the interested data<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> img_data = img.get_fdata()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> img_sobel_data = img_sobel.get_fdata()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> header = img.header<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> nb_img = header.get_data_shape()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR">
</span><span style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR">nb_img_h = nb_img[2] #Hauteur<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR">
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR">for sl in range(0,nb_img_h):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> slice_h = img_data[:, :, sl]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> #Sobel<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> sx = ndimage.sobel(slice_h, axis=0, mode='constant')<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> sy = ndimage.sobel(slice_h, axis=1, mode='constant')<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> sobel_h = np.hypot(sx, sy)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"> img_sobel_data[:, :, sl] = sobel_h #Change the image slice to the sobel one<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR"># Save Sobel:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";mso-fareast-language:FR">nib.save(img_sobel,imSobel_path)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">So my question now : How to change the NIFTI image get from img_sobel.get_fdata() ?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Have a nice week !<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="mso-fareast-language:FR">De :</span></b><span style="mso-fareast-language:FR"> PLANTIN Baptiste
<br>
<b>Envoyé :</b> vendredi 28 février 2020 15:22<br>
<b>À :</b> 'neuroimaging@python.org' <neuroimaging@python.org><br>
<b>Objet :</b> 2 questions about Image processing on nifti images<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">Hello team,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Looking recently about MRI, I’m starting to work using your tool and I have two questions, one relative to a method and one about dataset nii.gz :<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l1 level1 lfo2"><![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">I’m actually use the Sobel filter on a .nii slices. If the process is successfully done, I don’t know how to create a new nifty image as a Sobel version of the original one. I tried this method:<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo4">
<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">Load the original nifty image as “img”<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo4">
<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">Load again the original image as “Sobel”
<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo4">
<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">Use the Sobel filtering on each slices<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo4">
<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">For each slices (for loop), replace the slice in “Sobel” to the new filtered slice<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo4">
<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">Save the new Sobel image in the file as “imSobelNumX”<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">This method don’t work, it seems the slices are not replaced. It is due to the particular format or it is due to Python compiler ?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l1 level1 lfo2"><![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">Is there are a nii.gz dataset of the entire (And healthy) body somewhere in order to use it as reference for detection ? I found only a GIF in internet actually (<a href="http://www.madsci.org/~lynn/VH/Transverse.gif">http://www.madsci.org/~lynn/VH/Transverse.gif</a>)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D;mso-fareast-language:FR">Thank you and best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D;mso-fareast-language:FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#007EAF;mso-fareast-language:FR">Cordialement,<br>
Baptiste PLANTIN <o:p></o:p></span></b></p>
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