External Email - Use Caution mri_gtmpvc --i ADNI-PET.nii --reg template.reg.lta --psf 6 --seg gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --mgx .01 --o gtmpvc.output I am trying to do like that. I tried to change the --seg gtmseg.mgz by aparc+aseg.mgz to obtain the 45 subcortical regions but it doesn't work PS: does mri_gtmpvc compute SUV? or the mean intensity?
Le dim. 19 juin 2022 à 20:55, Douglas N. Greve <dgr...@mgh.harvard.edu> a écrit : > what is your mri_gtmpvc command line? > > On 6/19/2022 2:22 PM, Bouchra Guelib wrote: > > External Email - Use Caution > These are the missing regions in which I want to obtain their SUVr. > Left-Lateral-Ventricle, Left-Inf-Lat-Vent, > 3rd-Ventricle, 4th-Ventricle, Left-vessel, Right-Lateral-Ventricle, > Right-Inf-Lat-Vent, 5th-Ventricle, WM-hypointensities, > Left-WM-hypointensities, > Right-WM-hypointensities, non-WM-hypointensities, > Left-non-WM-hypointensities, Right-non-WM-hypointensities, Optic-Chiasm, > CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, CC_Anterior. > > This is what I get when I apply mri_gtmpvc. > I already followed the link that you submitted to me. > > > Le dim. 19 juin 2022 à 15:54, Douglas N. Greve <dgr...@mgh.harvard.edu> a > écrit : > >> >> >> On 6/15/2022 7:40 AM, Bouchra Guelib wrote: >> >> External Email - Use Caution >> Hi, >> I wonder if someone can help me to do something similar to that: >> " the mean intensity of each FreeSurfer region (ROI) for the 45 >> subcortical and the 68 cortical regions were assessed the mean intensity >> of each FreeSurfer region (ROI) for the 45 subcortical and the 68 cortical >> regions were assessed to obtain SVU". >> Also, I found an article that mentioned that " the estimated total >> intracranial volume (eTIV) is calculated, which is used later for >> normalization of the volumetric measures". >> My questions are: >> 1) In " gtm.stats.dat" not all subcortical regions are mentioned, why? >> >> which ones are missing? >> >> 2) I applied "mri_getmpc" to obtain the mean intensity, however, I could >> not figure out what I should do after this step to obtain the mean >> intensity and compute SVU. >> >> Do you mean mri_gtmpvc? the values will be in the gtm.stats.dat file >> >> 3) why do they use eTIV, should I use it, and if yes how! >> >> I don't know. It does not make sense to correct an intensity with eTIV. >> btw, I assume you've seen this page *MailScanner has detected a >> possible fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1Uwp6lqNIFYyMl7qCT0DRzJdCfBXpZ_PqAT03oufoXMOCmfTKDsgNj8jaC1dzep1pBNeDYtES5H43hYZqCXRTuwkwkNjW1h6Q_wu8-UxFbYj24MFG9t15d2quQ6cR_oqdhLCx07J6NItrM-3lPFByjlqKUC_X072lDVhi--_w6wOkewwapm5ZOY7dK7A9EBflGMt0rP7TpMKGZ0MBVi9SxsMILPX8bKSnZYCopBXMx4Qw-ti9VRoZy6_CVKH5M9oTPjl8hKGUs67IdktWXOdXVU2WmfhChGienWTmQopA_xq1hPHUkt_pHqhCWJmpP4BJshihlu1HvHAY7_AHiF3L_A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer >> <https://secure-web.cisco.com/11lfuSnUl9w3h9Z18W6RjGbXg4yDv-3fW_VwCgPcK0MKpqIEgwfHSpVaj1YEx5PJfyFc68G0JtWihX6t3diQDXq8yaFQO9Je6SCNJYp-EeRtsGEzqIgHqfAOD0k51ASu89BiIu9TkU8w64pAJ6IAJBkfKYKW4qnakZIHQwje9eQRI80k8Lf_Y85maOKCcT0MNsdkyXw3wTk0fbbLy2z3bf6yDl7hz3Gjaz9i1azyger-vXc5sW10n9afmkMiMHj3-NxiHVryG3AqHBkAJgVSKoy3ZmHETymKPmXmWNOpt3OdL7H_LaYVYsA6ZbQ6MgzhA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer> >> ? >> >> best regards. >> >> >> -- >> *GUELIB Bouchra: *Ph.D. student >> *Lire *Laboratory >> University: Constantine 2-Abdelhamid Mehri- *Algeria * >> Alternative email: guelibbouc...@gmail.com >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/12hUR_wpMO1uuT6RewLJPcbr98hMJrakuwp4YOQxU1HThbyUVOGfhaW2LTuEiLYuF8T-CVqLFZkmHCiSx2ie34dA4CXOcWbL2QxItfVzvMwgYzpeIgrPufqgOiZFO1gYvI1uA5aEfed7rvNPejQMZaoqUGk7MoKnbQUg1LJpkBFlYz0X93twMUuqs9Aq0-u-NNiHwbOWi8ya7fZ6KlySjeGL5inEiv2L3ZqFROhtMzXp5UBxBTP2Iyurmu-qEtDZx25OKeOeypSDjDLJ7QjhO0Y2zKimEQ30KSKW6F7QL80gJJh2iATSkRNb1x_uEcajhcfHl49k-DAYpg87G954_3A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1tJiVW4DA6nl89NLr1MA90ucm75k1Qj4zjYs9bBZl9TfjL89btPtk52_q-FUE52664jSIoJsQQo_HNgJEyTaHCUEMFub25rNL8Yash3BD9qNu_EMdV0MsltQdlNnvVuhGOcs-RNOeKx6-4LpVpjY3BAXxMfpVYgNx3vFjZHe8yM3TZUuk5pxkvIWJOQZZWYcNBuy5WBrwp6fDiyWfXcMVE3laalCdbzmiXk11yZ6Vb27DMnuAhYOoc6dFXpF1D8G0LZSoeNq7RdvX--jWjauQWA8OEQbFxpNHt7AaAHzbBFvaMmfDIdE4cjUsutWX77Iz/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/12hUR_wpMO1uuT6RewLJPcbr98hMJrakuwp4YOQxU1HThbyUVOGfhaW2LTuEiLYuF8T-CVqLFZkmHCiSx2ie34dA4CXOcWbL2QxItfVzvMwgYzpeIgrPufqgOiZFO1gYvI1uA5aEfed7rvNPejQMZaoqUGk7MoKnbQUg1LJpkBFlYz0X93twMUuqs9Aq0-u-NNiHwbOWi8ya7fZ6KlySjeGL5inEiv2L3ZqFROhtMzXp5UBxBTP2Iyurmu-qEtDZx25OKeOeypSDjDLJ7QjhO0Y2zKimEQ30KSKW6F7QL80gJJh2iATSkRNb1x_uEcajhcfHl49k-DAYpg87G954_3A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1tJiVW4DA6nl89NLr1MA90ucm75k1Qj4zjYs9bBZl9TfjL89btPtk52_q-FUE52664jSIoJsQQo_HNgJEyTaHCUEMFub25rNL8Yash3BD9qNu_EMdV0MsltQdlNnvVuhGOcs-RNOeKx6-4LpVpjY3BAXxMfpVYgNx3vFjZHe8yM3TZUuk5pxkvIWJOQZZWYcNBuy5WBrwp6fDiyWfXcMVE3laalCdbzmiXk11yZ6Vb27DMnuAhYOoc6dFXpF1D8G0LZSoeNq7RdvX--jWjauQWA8OEQbFxpNHt7AaAHzbBFvaMmfDIdE4cjUsutWX77Iz/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at *MailScanner has detected a possible >> fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1NzZ5GtkwhuVjw6mK7IXkjfn61WoTiUMX2TYGwl4KxFOXAuHPQwD04vNKeCpMmOxBoHVFzM0sLxEH1qLx_QMnxH-_WkESNs0ztOSBUyPqLND9pi5xczhxBgvZGXYsFCAnsewkYnduCGdD6CHx-z-17n2S5vsF6i8tswMMk7XPM9j8xjARl2GHYxN0xkHFxxIL-r910JF5lAobOJdZSJKlly1D0GGGx_ZeMbcW3ArqSE9AbJIasXYwEU3YIhIR2fLD5gqk_U9EDfuz48YRprM98kzXITX-pbPVWAP0HHDlJX24xQQs9Rai--a5YxhnWquSv_MjhixLze9YLCnQ4KcLcA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> <https://secure-web.cisco.com/1-LW5vdxo_6MoxyzhjE3GUr083cAKQ778OCcgM09Un7fu-nicaUFDVuF7xkazptqXDmw4WmSLeoAmO_H-zs-p394x9SGkdgQ2IWT4EZ9Z5D71xWX7uVoJLC6aGW829xU1GbCeC5zbxqOusgJ4KeUZ6vmoHwbE0NOHy2vG0Nvn-uStJL_SSrFICazbieYi02iZN9u0deKD9dXg--BKgc3QfvrzVEVcfleaCfAP3fnt1tF5f0232H4v9mi4lBp2eZUBPWFgAnvIz4fhYS0RyaKDoySYaC70OxA6VgtenFlxUHCrcAbQr5mXNGwe0bBmpaEm/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >> <*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1NzZ5GtkwhuVjw6mK7IXkjfn61WoTiUMX2TYGwl4KxFOXAuHPQwD04vNKeCpMmOxBoHVFzM0sLxEH1qLx_QMnxH-_WkESNs0ztOSBUyPqLND9pi5xczhxBgvZGXYsFCAnsewkYnduCGdD6CHx-z-17n2S5vsF6i8tswMMk7XPM9j8xjARl2GHYxN0xkHFxxIL-r910JF5lAobOJdZSJKlly1D0GGGx_ZeMbcW3ArqSE9AbJIasXYwEU3YIhIR2fLD5gqk_U9EDfuz48YRprM98kzXITX-pbPVWAP0HHDlJX24xQQs9Rai--a5YxhnWquSv_MjhixLze9YLCnQ4KcLcA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> <https://secure-web.cisco.com/1-LW5vdxo_6MoxyzhjE3GUr083cAKQ778OCcgM09Un7fu-nicaUFDVuF7xkazptqXDmw4WmSLeoAmO_H-zs-p394x9SGkdgQ2IWT4EZ9Z5D71xWX7uVoJLC6aGW829xU1GbCeC5zbxqOusgJ4KeUZ6vmoHwbE0NOHy2vG0Nvn-uStJL_SSrFICazbieYi02iZN9u0deKD9dXg--BKgc3QfvrzVEVcfleaCfAP3fnt1tF5f0232H4v9mi4lBp2eZUBPWFgAnvIz4fhYS0RyaKDoySYaC70OxA6VgtenFlxUHCrcAbQr5mXNGwe0bBmpaEm/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> >> . >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> > > > -- > *GUELIB Bouchra: *Ph.D. student > *Lire *Laboratory > University: Constantine 2-Abdelhamid Mehri- *Algeria * > Alternative email: guelibbouc...@gmail.com > > > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/12hUR_wpMO1uuT6RewLJPcbr98hMJrakuwp4YOQxU1HThbyUVOGfhaW2LTuEiLYuF8T-CVqLFZkmHCiSx2ie34dA4CXOcWbL2QxItfVzvMwgYzpeIgrPufqgOiZFO1gYvI1uA5aEfed7rvNPejQMZaoqUGk7MoKnbQUg1LJpkBFlYz0X93twMUuqs9Aq0-u-NNiHwbOWi8ya7fZ6KlySjeGL5inEiv2L3ZqFROhtMzXp5UBxBTP2Iyurmu-qEtDZx25OKeOeypSDjDLJ7QjhO0Y2zKimEQ30KSKW6F7QL80gJJh2iATSkRNb1x_uEcajhcfHl49k-DAYpg87G954_3A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1NzZ5GtkwhuVjw6mK7IXkjfn61WoTiUMX2TYGwl4KxFOXAuHPQwD04vNKeCpMmOxBoHVFzM0sLxEH1qLx_QMnxH-_WkESNs0ztOSBUyPqLND9pi5xczhxBgvZGXYsFCAnsewkYnduCGdD6CHx-z-17n2S5vsF6i8tswMMk7XPM9j8xjARl2GHYxN0xkHFxxIL-r910JF5lAobOJdZSJKlly1D0GGGx_ZeMbcW3ArqSE9AbJIasXYwEU3YIhIR2fLD5gqk_U9EDfuz48YRprM98kzXITX-pbPVWAP0HHDlJX24xQQs9Rai--a5YxhnWquSv_MjhixLze9YLCnQ4KcLcA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1NzZ5GtkwhuVjw6mK7IXkjfn61WoTiUMX2TYGwl4KxFOXAuHPQwD04vNKeCpMmOxBoHVFzM0sLxEH1qLx_QMnxH-_WkESNs0ztOSBUyPqLND9pi5xczhxBgvZGXYsFCAnsewkYnduCGdD6CHx-z-17n2S5vsF6i8tswMMk7XPM9j8xjARl2GHYxN0xkHFxxIL-r910JF5lAobOJdZSJKlly1D0GGGx_ZeMbcW3ArqSE9AbJIasXYwEU3YIhIR2fLD5gqk_U9EDfuz48YRprM98kzXITX-pbPVWAP0HHDlJX24xQQs9Rai--a5YxhnWquSv_MjhixLze9YLCnQ4KcLcA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: guelibbouc...@gmail.com
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
