Thank you all! If you have made additional improvements to the module, please let me know. In particular, I am looking to see y-axis units displayed, possible color map of D/D*/f, additional maps based on simple product or division, like f x D*, D*/D vs b etc. to name a few. Any possibility to connect "f" with fractional moving blood volume.
Thank you so very much for providing IVIM module. -Anil From: Maier-Hein, Klaus H. [mailto:k.maier-h...@dkfz-heidelberg.de] Sent: Tuesday, September 24, 2019 4:16 AM To: Neher, Peter <p.ne...@dkfz-heidelberg.de>; Shetty, Anil <ashe...@bcm.edu>; mitk-users@lists.sourceforge.net Subject: AW: [mitk-users] IVIM module Hi, I recall that there are several (non MITK) papers considering different methods. However, to do it directly in MITK, this would require taking a good look at the implementation. I think, only the default method ist really nicely tested. Cheers, Klaus Von: Neher, Peter Gesendet: Dienstag, 24. September 2019 08:45 An: Shetty, Anil <ashe...@bcm.edu<mailto:ashe...@bcm.edu>>; mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>; Maier-Hein, Klaus H. <k.maier-h...@dkfz-heidelberg.de<mailto:k.maier-h...@dkfz-heidelberg.de>> Betreff: AW: [mitk-users] IVIM module I'm not sure about that. I know that quite some papers were published using the IVIM methods implemented in MITK, but I don't know about a comparative study of the different fits. Do you know about anything like that, Klaus? Peter ________________________________ Von: Shetty, Anil <ashe...@bcm.edu<mailto:ashe...@bcm.edu>> Gesendet: Montag, 23. September 2019 17:15 An: Neher, Peter; mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Betreff: RE: [mitk-users] IVIM module Thank you very much Peter, for clarification. I do appreciate your timely response. Has there been any study done to compare different methods you propose in IVIM analysis? How do you determine which method provides the best estimation of D/D*/f? I mean between (3 parameter fit vs. fixed D* then D and f etc,.) Thank you for your help Regards, Anil N. Shetty, Ph.D. Associate Professor Baylor College of Medicine Department of Obstetrics and Gynecology Pavilion for women Texas Children's Hospital 6651 Main Street/Suite F1040-18 Houston, TX 77030 832-826-7312 (Direct) 832-825-9351 (Fax) From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de] Sent: Monday, September 23, 2019 2:05 AM To: Shetty, Anil <ashe...@bcm.edu<mailto:ashe...@bcm.edu>>; mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Subject: AW: [mitk-users] IVIM module ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. ________________________________ Dear Anil, only the weighted measurements are plotted, i.e. b>0. But anyway, only the scale, so the positions on the y-axis, is logarithmic, no the shown values. So you plot ln(s/s0), but the axis label still shows s/s0. Just a matter of visualization. Peter ________________________________ Von: Shetty, Anil <ashe...@bcm.edu<mailto:ashe...@bcm.edu>> Gesendet: Samstag, 21. September 2019 12:59 An: Neher, Peter Betreff: Re: [mitk-users] IVIM module Hi Peter: Thank you for your help with IVIM module. BTW, I have slight confusion here. If the signal is plotted with "Ln(S/S0)"on the y-axis, the first point at b =0 should be =0, since S/S0 =1 at b =0. How do you reverse it to show max on y-axis =1 at b =0 in your plot? S = S0exp(-bD) mono-exponential at low b-values. Ln(S/S0) = -bD >From plot at b =0, L(s/S0) = 0 Am I missing something? Thanks Anil ________________________________ From: Neher, Peter <p.ne...@dkfz-heidelberg.de<mailto:p.ne...@dkfz-heidelberg.de>> Sent: Friday, September 20, 2019 02:14 AM To: Shetty, Anil <ashe...@bcm.edu<mailto:ashe...@bcm.edu>>; mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> <mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>> Subject: AW: [mitk-users] IVIM module Or rather S/S_0, but the scale is logarithmic. ________________________________________ Von: Neher, Peter <p.ne...@dkfz-heidelberg.de<mailto:p.ne...@dkfz-heidelberg.de>> Gesendet: Freitag, 20. September 2019 08:56 An: Shetty, Anil; mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Betreff: Re: [mitk-users] IVIM module ln(s) I will see to it that this will be indicated in the plot. Peter ________________________________________ Von: Shetty, Anil <ashe...@bcm.edu<mailto:ashe...@bcm.edu>> Gesendet: Donnerstag, 19. September 2019 17:27 An: Neher, Peter Betreff: RE: [mitk-users] IVIM module Hi Peter: One more thing. The plot in figure, is that "Signal vs b" or "Ln(Signal) vs b" ? Thanks -Anil -----Original Message----- From: Neher, Peter [mailto:p.ne...@dkfz-heidelberg.de] Sent: Thursday, September 19, 2019 8:47 AM To: Shetty, Anil <ashe...@bcm.edu<mailto:ashe...@bcm.edu>>; mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>; Götz, Michael <m.go...@dkfz-heidelberg.de<mailto:m.go...@dkfz-heidelberg.de>>; Jäger, Paul <p.jae...@dkfz-heidelberg.de<mailto:p.jae...@dkfz-heidelberg.de>> Subject: AW: [mitk-users] IVIM module Dear Anil, If I look at the code, the method actually does a 3-parameter LM fit: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_MIC-2DDKFZ_MITK-2DDiffusion_blob_master_Modules_DiffusionCore_Algorithms_Reconstruction_itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp-23L447&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=7rs0ek8jQUqY_tKDw4FmWBioHKPqbVI2nz7tkl14xyM&e= I am not sure where the output on the clipboard originates from. Do you know anything about this, Michael & Paul? Peter ________________________________________ Von: ashetty <ashe...@bcm.edu<mailto:ashe...@bcm.edu>> Gesendet: Mittwoch, 18. September 2019 18:55 An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Betreff: [mitk-users] IVIM module I have been using IVIM module to determine f, D and D* using 3-parameter fit. However, when I copy measurement points to excel, I see that it does first linear fit of D and f at high b, and then, fits for D*. Should this not do 3 parameters simultaneously using L-M method when I choose option of 3-parameter fit? Appreciate your answer. _anil -- Sent from: https://urldefense.proofpoint.com/v2/url?u=http-3A__mitk-2Dusers.1123740.n5.nabble.com_&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=tRN1QFquy_aNi79SNJJDlv8XtYG0IK5q3-k1LYQnzU8&e= _______________________________________________ mitk-users mailing list mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_mitk-2Dusers&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=RsPQxKza4BsCqlriISy6MlMZ1ZZNLO8-ysVRB2b_koY&s=8d-vo07FfYJigUbg-VF3z8WO1PTdEs1EifBqZ_xf17Q&e= _______________________________________________ mitk-users mailing list mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_mitk-2Dusers&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=xunJOi6tH8YusoQF3t9EDA&m=WM7OiABjV744a2ejcTzW2Pt0Gmq5WD9nHV3cdqDDLyk&s=G7JXaFm6cQSZxS-18uPRBs0jnIqcc__a6vvLb77tpco&e=
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