Try following that workflow but don't use --default-seg-merge
On 6/24/2022 4:54 PM, Bouchra Guelib wrote:
External Email - Use CautionI would like to follow the documentation, however I need all 45 subcortical regions which I can't get them using mri_gtmpvcLe ven. 24 juin 2022 à 15:32, Douglas N. Greve <dgr...@mgh.harvard.edu> a écrit :This is not the workflow that we support. Follow the workflow in the petsurfer documentation is you want assistance. On 6/21/2022 4:40 AM, Bouchra Guelib wrote:External Email - Use Caution Hi, I want to register PET to T1 MRI using FSL dof12 then I want to extract the SUV. I would like you to help me on these lines Firstly I converted my MRI named ADNI.nii T1 to min305 space then I applied recon-all. The output is the Folder ADNI Then I want to register my PET to T1 MRI so I use these line bbregister --s ADNI --init-fsl --t2 --mov PET.nii --reg Pet2T1.register.dof12.dat --lta Pet2T1.register.dof12.lta --init-reg-out Pet2T1 here I want to extract SUV so used this commend mri_segstats --seg ADNI/mri/aparc+aseg.mgz --sum petsuv.segstats.dat --i PET.nii --ctab-default the CMD displays ERROR: dimension mismatch between input volume and seg input 128 128 90 seg 256 256 256 Would tell me where is my mistakes Le dim. 19 juin 2022 à 22:43, Douglas N. Greve <dgr...@mgh.harvard.edu> a écrit : You can try removing --default-seg-merge, but it may fail. It can compute a relative SUV (relative to a give n ROI). By default, this will be pons, but you can chose others. SUV requires knowing things like the patients weight. On 6/19/2022 4:15 PM, Bouchra Guelib wrote: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 applymri_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 file3) 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://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer <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 list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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