Rosella

Good morning, I am a researcher at University of Genoa, Italy, in the field of neuroimaging. I am introducing to the rs-fMRI field applied to mice brain data. Specifically, I am going into details of the work Explainable fuzzy clustering framework reveals divergent default mode network connectivity dynamics in schizophrenia (https://pubmed.ncbi.nlm.nih.gov/36824777/) and trying to reproduce its step applied to mice brain. In this regard, I was wondering if the Neuromark pipeline of the Group ICA...

Good morning, I am a researcher at University of Genoa, Italy, in the field of neuroimaging. I am introducing to the rs-fMRI field applied to mice brain data. Specifically, I am going into details of the work Explainable fuzzy clustering framework reveals divergent default mode network connectivity dynamics in schizophrenia (https://pubmed.ncbi.nlm.nih.gov/36824777/) and trying to reproduce its step applied to mice brain. In this regard, I was wondering if the Neuromark pipeline of the Group ICA...

ok. thank you Rosella https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail Mail priva di virus. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> Il giorno ven 13 mar 2020 alle ore 19:29 Nick Tustison ntustison@users.sourceforge.net ha scritto: Yes, please do. But you shouldn't have to install ITK separately. I don't know why this happens...

However, I wonder why this happens just for 4 subjects out of 40 I processed. Il ven 13 mar 2020, 18:32 Nick Tustison ntustison@users.sourceforge.net ha scritto: No, rescaling won't help. Coincidentally I ran into this awhile back and I had to recompile from source. I suspect that something happened upstream in ITK proper causing this issue in the N4 class. output of N4 is black https://sourceforge.net/p/advants/discussion/840261/thread/e9dae6218c/?limit=25#6d1a/fda6 Sent from sourceforge.net because...

ok thank yo. So do you suggest reinstalling itk and ants? Thanks Rosella Il ven 13 mar 2020, 18:32 Nick Tustison ntustison@users.sourceforge.net ha scritto: No, rescaling won't help. Coincidentally I ran into this awhile back and I had to recompile from source. I suspect that something happened upstream in ITK proper causing this issue in the N4 class. output of N4 is black https://sourceforge.net/p/advants/discussion/840261/thread/e9dae6218c/?limit=25#6d1a/fda6 Sent from sourceforge.net because...

Even using ITK-SNAP the image after bias field correction appears black. when launching the command the following warning appears: rosella@vivi:/media/rosella/TOSHIBA EXT/brain_mblesa/Subjects/T1/bfc$ N4BiasFieldCorrection -d 3 -i ../rFOV/3dT1_8_normalized.nii.gz -x ../bet/3dT1_8_normalized_bet_mask.nii.gz -o [3dT1_8_corr.nii, 3dT1_8_bias.nii] -c [50x50x50,0.001] -s 2 -b [100,3] -t [0.15,0.01,200] -v 1 Running N4 for 3-dimensional images. Original intensity range: [0, 662] Warning: Your input image...

Even using ITK-SNAP the image after bias field correction appears black. when launching the command the following warning appears: rosella@vivi:/media/rosella/TOSHIBA EXT/brain_mblesa/Subjects/T1/bfc$ N4BiasFieldCorrection -d 3 -i ../rFOV/3dT1_8_normalized.nii.gz -x ../bet/3dT1_8_normalized_bet_mask.nii.gz -o [3dT1_8_corr.nii, 3dT1_8_bias.nii] -c [50x50x50,0.001] -s 2 -b [100,3] -t [0.15,0.01,200] -v 1 Running N4 for 3-dimensional images. Original intensity range: [0, 662] Warning: Your input image...

I am using mrview , a Mrtrix3 tool . WIth other subjects N4 output is visible and not black! thanks, Rosella Il giorno ven 6 mar 2020 alle ore 17:00 Nick Tustison ntustison@users.sourceforge.net ha scritto: Okay, so what are you using to view the results? If you're not using ITK-SNAP, please use that program to verify that the problem is not with the viewer. output of N4 is black https://sourceforge.net/p/advants/discussion/840261/thread/e9dae6218c/?limit=25#4c8f/f02e/9092/c0c5/a42f/d283 Sent from...