From SyedQasim.Abbas at latrobe.edu.au Tue Feb 25 05:25:59 2020 From: SyedQasim.Abbas at latrobe.edu.au (Syed Qasim Abbas) Date: Tue, 25 Feb 2020 10:25:59 +0000 Subject: [Neuroimaging] Need help for cerebellum removal Message-ID: Hi, I am trying to remove cerebellum from my MRI image for further analysis, but I am unable to find any suitable tool for this purpose. Please suggest me a suitable tool that can remove cerebellum from any MRI nifty image. I shall be very thankful to you for your encouraging suggestion. Thanks Regards Qasim, PhD student La Trobe University -------------- next part -------------- An HTML attachment was scrubbed... URL: From baptiste.plantin at altran.com Fri Feb 28 09:21:31 2020 From: baptiste.plantin at altran.com (PLANTIN Baptiste) Date: Fri, 28 Feb 2020 14:21:31 +0000 Subject: [Neuroimaging] 2 questions about Image processing on nifti images Message-ID: <42E126B2488FED44A5647DC18C0D5D10DB4B71DF@XMB-DCFR-35.europe.corp.altran.com> Hello team, 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 : - 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: ? Load the original nifty image as "img" ? Load again the original image as "Sobel" ? Use the Sobel filtering on each slices ? For each slices (for loop), replace the slice in "Sobel" to the new filtered slice ? Save the new Sobel image in the file as "imSobelNumX" 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 ? - 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 (http://www.madsci.org/~lynn/VH/Transverse.gif) Thank you and best regards, Cordialement, Baptiste PLANTIN Ing?nieur Consultant ALTRAN IDF baptiste.plantin at altran.com [cid:image003.jpg at 01D2E8E2.CBD89F30] 2, rue Paul Dautier 78457 V?lizy Villacoublay FRANCE www.altran.com/fr [cid:image004.jpg at 01D2E8E2.CBD89F30] [cid:image005.jpg at 01D2E8E2.CBD89F30] [cid:image006.jpg at 01D2E8E2.CBD89F30] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 1892 bytes Desc: image001.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 759 bytes Desc: image002.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.jpg Type: image/jpeg Size: 718 bytes Desc: image003.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image004.jpg Type: image/jpeg Size: 745 bytes Desc: image004.jpg URL: From matthew.brett at gmail.com Sat Feb 29 08:09:50 2020 From: matthew.brett at gmail.com (Matthew Brett) Date: Sat, 29 Feb 2020 13:09:50 +0000 Subject: [Neuroimaging] 2 questions about Image processing on nifti images In-Reply-To: <42E126B2488FED44A5647DC18C0D5D10DB4B71DF@XMB-DCFR-35.europe.corp.altran.com> References: <42E126B2488FED44A5647DC18C0D5D10DB4B71DF@XMB-DCFR-35.europe.corp.altran.com> Message-ID: Hi, On Sat, Feb 29, 2020 at 1:02 PM PLANTIN Baptiste wrote: > > Hello team, > > > > 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 : > > - 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: > > ? Load the original nifty image as ?img? > > ? Load again the original image as ?Sobel? > > ? Use the Sobel filtering on each slices > > ? For each slices (for loop), replace the slice in ?Sobel? to the new filtered slice > > ? Save the new Sobel image in the file as ?imSobelNumX? Could you post the code that you are using? The general idea is: img = nib.load('my_image.nii') data = img.get_fdata() for z_no in range(data.shape[-1]): data[..., z_no] = some_filter(data[..., z_no]) new_img = nib.Nifti1Image(data, None, img.header) nib.save(new_img, 'filtered_image.nii') Cheers, Matthew