From elizabeth.lyde at mavs.uta.edu Tue Jan 16 10:14:47 2018 From: elizabeth.lyde at mavs.uta.edu (Lyde, Elizabeth) Date: Tue, 16 Jan 2018 15:14:47 +0000 Subject: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points Message-ID: Hello all, I was curious if anyone has had success obtaining the HbO /HbR concentration overlay on Atlas using digitizing points rather than probe.SD files. Or more simply, is there a way to convert the digitizing points into the probe.SD file? Any advice or suggestions would be greatly appreciated. Elizabeth -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20180116/66156282/attachment.html From elizabeth.lyde at mavs.uta.edu Tue Jan 16 17:41:07 2018 From: elizabeth.lyde at mavs.uta.edu (Lyde, Elizabeth) Date: Tue, 16 Jan 2018 22:41:07 +0000 Subject: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points In-Reply-To: References: Message-ID: Hello again, It turns out that the digpts.txt file can be used instead of the probe.SD file when trying to obtain Hb concentration plots via AtlasViewer as long as the groupResults file is also present. I am now facing an issue where after clicking tools>>Hb Conc Overlay and adding the time range [tRangeMin tRangeMax], my meansList channels change from yellow to green. I'm unsure if this indicates an error has occur, or that it has processed the block average. In addition, the brain disappears and I am unable to get HbO overlay. The Colormap Thresh range is [NaN NaN]. I can manually change the Colormap Thresh; however, nothing still appears. (The HRF had a range between -1.5 and 1.5 microMolar in HomER.) Does anyone have advice as to why this may be happening? Many thanks, Elizabeth ________________________________ From: Lyde, Elizabeth Sent: Tuesday, January 16, 2018 9:14:47 AM To: moi moi Subject: HbO/HbR concentration changes overlay on the Atlas using Digitizing points Hello all, I was curious if anyone has had success obtaining the HbO /HbR concentration overlay on Atlas using digitizing points rather than probe.SD files. Or more simply, is there a way to convert the digitizing points into the probe.SD file? Any advice or suggestions would be greatly appreciated. Elizabeth -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20180116/5bfbb72d/attachment.html From lpolloni at central.uh.edu Fri Jan 19 09:44:13 2018 From: lpolloni at central.uh.edu (Pollonini, Luca) Date: Fri, 19 Jan 2018 14:44:13 +0000 Subject: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points In-Reply-To: References: Message-ID: <5FEBE48B-DAC5-4606-9C10-47996FD233FA@central.uh.edu> Hello Elizabeth, Jonathan Perry with my lab has been successful in overlaying Hb concentrations onto the standard brain. Since he is also busy working for NIRx, he might not be able to respond immediately, but I am confident he can provide some guidance soon. Best, Luca Luca Pollonini, Ph.D. Assistant Professor Department of Engineering Technology University of Houston 4734 Calhoun Rd., Room# 123 Houston, TX 77204-4021 Tel: (713) 743-4159 E-mail: lpollonini at uh.edu Web: polloninilab.com From: on behalf of "Lyde, Elizabeth" Reply-To: "homer-users at nmr.mgh.harvard.edu" Date: Thursday, January 18, 2018 at 6:15 AM To: moi moi Subject: Re: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points Hello again, It turns out that the digpts.txt file can be used instead of the probe.SD file when trying to obtain Hb concentration plots via AtlasViewer as long as the groupResults file is also present. I am now facing an issue where after clicking tools>>Hb Conc Overlay and adding the time range [tRangeMin tRangeMax], my meansList channels change from yellow to green. I'm unsure if this indicates an error has occur, or that it has processed the block average. In addition, the brain disappears and I am unable to get HbO overlay. The Colormap Thresh range is [NaN NaN]. I can manually change the Colormap Thresh; however, nothing still appears. (The HRF had a range between -1.5 and 1.5 microMolar in HomER.) Does anyone have advice as to why this may be happening? Many thanks, Elizabeth From: Lyde, Elizabeth Sent: Tuesday, January 16, 2018 9:14:47 AM To: moi moi Subject: HbO/HbR concentration changes overlay on the Atlas using Digitizing points Hello all, I was curious if anyone has had success obtaining the HbO /HbR concentration overlay on Atlas using digitizing points rather than probe.SD files. Or more simply, is there a way to convert the digitizing points into the probe.SD file? Any advice or suggestions would be greatly appreciated. Elizabeth -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20180119/4ca2fab7/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 2033 bytes Desc: image002.png Url : http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20180119/4ca2fab7/attachment-0001.png From elizabeth.lyde at mavs.uta.edu Sat Jan 20 16:52:36 2018 From: elizabeth.lyde at mavs.uta.edu (Lyde, Elizabeth) Date: Sat, 20 Jan 2018 21:52:36 +0000 Subject: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points In-Reply-To: <5FEBE48B-DAC5-4606-9C10-47996FD233FA@central.uh.edu> References: , <5FEBE48B-DAC5-4606-9C10-47996FD233FA@central.uh.edu> Message-ID: Thank you for letting me know. I truly appreciate it. Elizabeth ________________________________ From: homer-users-bounces at nmr.mgh.harvard.edu on behalf of Pollonini, Luca Sent: Friday, January 19, 2018 8:44:13 AM To: moi moi Subject: Re: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points Hello Elizabeth, Jonathan Perry with my lab has been successful in overlaying Hb concentrations onto the standard brain. Since he is also busy working for NIRx, he might not be able to respond immediately, but I am confident he can provide some guidance soon. Best, Luca Luca Pollonini, Ph.D. Assistant Professor Department of Engineering Technology University of Houston 4734 Calhoun Rd., Room# 123 Houston, TX 77204-4021 Tel: (713) 743-4159 E-mail: lpollonini at uh.edu Web: polloninilab.com From: on behalf of "Lyde, Elizabeth" Reply-To: "homer-users at nmr.mgh.harvard.edu" Date: Thursday, January 18, 2018 at 6:15 AM To: moi moi Subject: Re: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points Hello again, It turns out that the digpts.txt file can be used instead of the probe.SD file when trying to obtain Hb concentration plots via AtlasViewer as long as the groupResults file is also present. I am now facing an issue where after clicking tools>>Hb Conc Overlay and adding the time range [tRangeMin tRangeMax], my meansList channels change from yellow to green. I'm unsure if this indicates an error has occur, or that it has processed the block average. In addition, the brain disappears and I am unable to get HbO overlay. The Colormap Thresh range is [NaN NaN]. I can manually change the Colormap Thresh; however, nothing still appears. (The HRF had a range between -1.5 and 1.5 microMolar in HomER.) Does anyone have advice as to why this may be happening? Many thanks, Elizabeth From: Lyde, Elizabeth Sent: Tuesday, January 16, 2018 9:14:47 AM To: moi moi Subject: HbO/HbR concentration changes overlay on the Atlas using Digitizing points Hello all, I was curious if anyone has had success obtaining the HbO /HbR concentration overlay on Atlas using digitizing points rather than probe.SD files. Or more simply, is there a way to convert the digitizing points into the probe.SD file? Any advice or suggestions would be greatly appreciated. Elizabeth -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20180120/2199b4c8/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 2033 bytes Desc: image002.png Url : http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20180120/2199b4c8/attachment-0001.png From SJAHANI at mgh.harvard.edu Sat Jan 20 20:20:25 2018 From: SJAHANI at mgh.harvard.edu (Jahani, Sahar) Date: Sun, 21 Jan 2018 01:20:25 +0000 Subject: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points In-Reply-To: <5FEBE48B-DAC5-4606-9C10-47996FD233FA@central.uh.edu> References: <5FEBE48B-DAC5-4606-9C10-47996FD233FA@central.uh.edu> Message-ID: Hello Elizabeth, Follow these steps (you need digpts and groupResults.mat in the same folder): 1. go to Tools --> Register Atlas to digpts, 2. register Probe to Surface, 3. go to Tools --> Hb Conc Overlay, 4. insert your desired tmin and tmax range. p.s: I am using Homer version v2.3 (https://www.nitrc.org/projects/homer2/) Hope this will help. Best, Sahar e: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points Hello Elizabeth, Jonathan Perry with my lab has been successful in overlaying Hb concentrations onto the standard brain. Since he is also busy working for NIRx, he might not be able to respond immediately, but I am confident he can provide some guidance soon. Best, Luca Luca Pollonini, Ph.D. Assistant Professor Department of Engineering Technology University of Houston 4734 Calhoun Rd., Room# 123 Houston, TX 77204-4021 Tel: (713) 743-4159 E-mail: lpollonini at uh.edu Web: polloninilab.com From: > on behalf of "Lyde, Elizabeth" > Reply-To: "homer-users at nmr.mgh.harvard.edu" > Date: Thursday, January 18, 2018 at 6:15 AM To: moi moi > Subject: Re: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points Hello again, It turns out that the digpts.txt file can be used instead of the probe.SD file when trying to obtain Hb concentration plots via AtlasViewer as long as the groupResults file is also present. I am now facing an issue where after clicking tools>>Hb Conc Overlay and adding the time range [tRangeMin tRangeMax], my meansList channels change from yellow to green. I'm unsure if this indicates an error has occur, or that it has processed the block average. In addition, the brain disappears and I am unable to get HbO overlay. The Colormap Thresh range is [NaN NaN]. I can manually change the Colormap Thresh; however, nothing still appears. (The HRF had a range between -1.5 and 1.5 microMolar in HomER.) Does anyone have advice as to why this may be happening? Many thanks, Elizabeth From: Lyde, Elizabeth Sent: Tuesday, January 16, 2018 9:14:47 AM To: moi moi Subject: HbO/HbR concentration changes overlay on the Atlas using Digitizing points Hello all, I was curious if anyone has had success obtaining the HbO /HbR concentration overlay on Atlas using digitizing points rather than probe.SD files. Or more simply, is there a way to convert the digitizing points into the probe.SD file? Any advice or suggestions would be greatly appreciated. Elizabeth -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20180121/9815b14d/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 180 bytes Desc: image002.png Url : http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20180121/9815b14d/attachment-0001.png From jorn at artinis.com Fri Jan 26 10:07:01 2018 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Fri, 26 Jan 2018 16:07:01 +0100 Subject: [Homer-users] ARTscientific: NIRS symposium in Thailand Message-ID: <006b01d396b7$515ac0c0$f4104240$@artinis.com> Dear Homerians, On June 27-30, we from Artinis Medical Systems are organizing a scientific symposium revolving around near-infrared spectroscopy (NIRS) for neuro- and sports research. We would like to invite you to register for the ARTscientific symposium in the beautiful and luxurious Wyndham Grand Phuket Kalim Bay in Thailand. In this 2.5-day symposium, we will create an open platform for both experienced and novice researchers to share experiences, discuss NIRS and enjoy several hands-on workshops. We are arranging an interesting line-up of keynote speakers, who will provide valuable insight into NIRS and brain research. Next to providing a NIRS playground we will organize poster and presentation sessions, so you will get the chance to present and discuss your research. To sum it all up social wining and dining will be organized in one of the most extraordinary places in Thailand. The registration: Get an early bird ticket The amount of rooms in the hotel are limited, so get yours quickly and benefit until February 28th from the early bird discount! Additional information on e.g. the program workshops or the location can be found on our website: http://www.artinis.com/artscientific-2018/. If you have any questions, suggestions or requests for the symposium, please do not hesitate to contact us at symposium at artinis.com. With best regards, The Artinis team -- J?rn M. Horschig, PhD Software Engineer & Project Leader NeuroGuard XS A Einsteinweg 17 6662PW Elst The Netherlands T +31 481 350 980 I www.artinis.com The information in this e-mail is confidential and intended solely for the person to whom it is addressed. If this message is not addressed to you, please be aware that you have no authorization to read this e-mail, to copy it, to furnish it to any person other than the addressee, or to use or misuse its content in any way whatsoever. Should you have received this e-mail by mistake, please bring this to the attention of the sender, after which you are kindly requested to destroy the original message. Sign up for our NIRS newsletter -------------- next part -------------- An HTML attachment was scrubbed... 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