External Email - Use Caution
Hello,
I'm trying to perform a pet ROI analysis on an image recon from a T1. I have to perform the analysis without normalization and partial volume correction. I'm having problems with regions with few or no voxels which makes me think I'm doing the analysis completely wrong .
With this command I obtain negative values for these regions:
mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1 .01 --mgx .01 --o $GTM_DIR/gtmpvc_PET.output
While with this I get many counts even for regions without voxels:
mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1.01 --no-tfe --o $GTM_DIR/gtmpvc_PET.output
Could you help me understand my mistake. Thank you very much. Parodi Matteo.
I will insert the commands I used before the ROI analysis:
recon-all -s Subj -i $IMAGED -all -threads 10
gtmseg --keep-cc --s Subj --xcerseg --o gtmseg100.mgz
mri_coreg --s Subj --mov ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --threads 10
External Email - Use Caution
I'm not sure what problem you are describing. Can you elaborate?
On 9/25/2023 9:16 AM, Matteo Parodi wrote:
External Email - Use Caution
Hello,
I'm trying to perform a pet ROI analysis on an image recon from a T1. I have to perform the analysis without normalization and partial volume correction. I'm having problems with regions with few or no voxels which makes me think I'm doing the analysis completely wrong .
With this command I obtain negative values for these regions:
mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1 .01 --mgx .01 --o $GTM_DIR/gtmpvc_PET.output
While with this I get many counts even for regions without voxels:
mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1.01 --no-tfe --o $GTM_DIR/gtmpvc_PET.output
Could you help me understand my mistake. Thank you very much. Parodi Matteo.
I will insert the commands I used before the ROI analysis:
recon-all -s Subj -i $IMAGED -all -threads 10
gtmseg --keep-cc --s Subj --xcerseg --o gtmseg100.mgz
mri_coreg --s Subj --mov ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --threads 10
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/130oL3BnVVBTfSNqrES16kNcrf8bAhTRKPdlgvp_vOk-CLW...
External Email - Use Caution
Sure I try, thank you for the replay.
I'm using the above-mentioned analisis to obtain the Uptake for the region in Desikan atlas, but the results are strange. I think the error is in the last command but I'm not sure.
The first time I had used mri command without --psf FWHM to not use Partial volume correction. mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1 .01 --mgx .01 --o $GTM_DIR/gtmpvc_PET.output But the result in gtm.stats.dat have some region ( those region with less voxel) with negative Uptake. Physically inconsistent but I had thought the problem was in the tissue fraction effect.
The second command uses the --no-tfe option like indicated in the wiki page, buth instead of negative count it returns high counts iven in regions indicated with 0 voxel. Again Physically inconsistent.
I tried different combination of the option to --auto-mask ang --mgx but it's not work differently or not at all. I don't have an idea of what and how the problem is, and not even where I can study to find the correct application metod.
Thank you for any suggestions you can give me.
Il giorno mar 26 set 2023 alle ore 16:03 Douglas N. Greve < dgreve@mgh.harvard.edu> ha scritto:
External Email - Use CautionI'm not sure what problem you are describing. Can you elaborate?
On 9/25/2023 9:16 AM, Matteo Parodi wrote:
External Email - Use CautionHello,
I'm trying to perform a pet ROI analysis on an image recon from a T1. I have to perform the analysis without normalization and partial volume correction. I'm having problems with regions with few or no voxels which makes me think I'm doing the analysis completely wrong .
With this command I obtain negative values for these regions:
mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1 .01 --mgx .01 --o $GTM_DIR/gtmpvc_PET.output
While with this I get many counts even for regions without voxels:
mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1.01 --no-tfe --o $GTM_DIR/gtmpvc_PET.output
Could you help me understand my mistake. Thank you very much. Parodi Matteo.
I will insert the commands I used before the ROI analysis:
recon-all -s Subj -i $IMAGED -all -threads 10
gtmseg --keep-cc --s Subj --xcerseg --o gtmseg100.mgz
mri_coreg --s Subj --mov ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --threads 10
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On 9/27/2023 10:17 AM, Matteo Parodi wrote:
External Email - Use Caution
Sure I try, thank you for the replay.
I'm using the above-mentioned analisis to obtain the Uptake for the region in Desikan atlas, but the results are strange. I think the error is in the last command but I'm not sure.
The first time I had used mri command without --psf FWHM to not use Partial volume correction. mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1 .01 --mgx .01 --o $GTM_DIR/gtmpvc_PET.output But the result in gtm.stats.dat have some region ( those region with less voxel) with negative Uptake. Physically inconsistent but I had thought the problem was in the tissue fraction effect.
This can and will happen since the GTM is just a general linear model trying to fit the data. It has no idea about what is physically realizable, and there are no constraints to enforce. This is just something that happens with the GLM at times.
The second command uses the --no-tfe option like indicated in the wiki page, buth instead of negative count it returns high counts iven in regions indicated with 0 voxel. Again Physically inconsistent.
I'm not sure what you mean
I tried different combination of the option to --auto-mask ang --mgx but it's not work differently or not at all. I don't have an idea of what and how the problem is, and not even where I can study to find the correct application metod.
Thank you for any suggestions you can give me.
Il giorno mar 26 set 2023 alle ore 16:03 Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
External Email - Use Caution I'm not sure what problem you are describing. Can you elaborate? On 9/25/2023 9:16 AM, Matteo Parodi wrote:External Email - Use Caution Hello, I'm trying to perform a pet ROI analysis on an image recon from a T1. I have to perform the analysis without normalization and partial volume correction. I'm having problems with regions with few or no voxels which makes me think I'm doing the analysis completely wrong . With this command I obtain negative values for these regions: mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1 .01 --mgx .01 --o $GTM_DIR/gtmpvc_PET.output While with this I get many counts even for regions without voxels: mri_gtmpvc --i ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --seg gtmseg100.mgz --no-rescale --auto-mask 1.01 --no-tfe --o $GTM_DIR/gtmpvc_PET.output Could you help me understand my mistake. Thank you very much. Parodi Matteo. I will insert the commands I used before the ROI analysis: recon-all -s Subj -i $IMAGED -all -threads 10 gtmseg --keep-cc --s Subj --xcerseg --o gtmseg100.mgz mri_coreg --s Subj --mov ${SUBJECTS_DIR}/PET.nii.gz --reg ${SUBJECTS_DIR}/PET.reg.lta --threads 10 _______________________________________________ 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/130oL3BnVVBTfSNqrES16kNcrf8bAhTRKPdlgvp_vOk-CLWBI7MJTg3a1rAmZ8oEZK7Cx8_mRKGAn9sdZGQhI58wbzlAhbon2lBJgdnIrzFX5205hwrIj_Srj2iK7W8oOCRdEHlAHpKPktdus316RyohDUC7p2-kzudZn5qCQqsJH6EcSQ5n49OC6RNHNcquXR_05uYmdz8r9fYWcWbSGqy3kCAatDHipMnCGV5NUqWinNcqPZ4gWRNoPSAm_l4bfb_gS4AD8OxTdWaVSScWTOQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1LRgc22WJyV47YTa9B7MuwU-ITZC5n5HdJelUiOz9QfXWEMo9pVL3Efd7mW_d4ssnDprZm2rMMljYAeizPA6ze9zv_gI4LlvqB0Ob0bQh0xJA9iNKE6-9nA2CMxD9CCkT86z_52cMhsqV3mgEVpT-Lb-ktBoz0izWug07BKIQugXldCo9fc3PsT6hRHoEN1yOlrRHC91j1Lt4G4z81NFBykoaPJKDW2dzG_iaamXg0iGSR7myCOEIXC8dWwObQYswxCdXHBE7PUs2A9axN8irQvZIpmt1Wn5S8paqAI8uB05Yr4mFdR9MPRwBSSbAsMoC/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://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1X6O6EKnVUxMY8BZ5GFxZr77CHYGIeLldmEpmcQY1_Zqt0sftwBm73MR5OGczKNtNZul150Ikg2UBEhOtPf4I9HM3LHgZS3Vwc8zjhjru-xbTgUa-8ljJJ-hu3HyqJtLFm9D5Rf7sBSNLQ3AfzgYUlq3mws0RLO_sTFbOoKIvW99xTaYRVXSfPD_8KUOgb4k_r72opbCo0l2O99M8TpC1Y3wjX_JsoNS449nltKhhMRLApvCzKF1cak-ZobDaIMBOAnNvaJ4vnN7Qb-Eb5aFVFzwiGDlzpLQxtxUVmO-idVGMuAs0n-ZUOKunjRZFJJQY/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1X6O6EKnVUxMY8BZ5GFxZr77CHYGIeLldmEpmcQY1_Zqt0sftwBm73MR5OGczKNtNZul150Ikg2UBEhOtPf4I9HM3LHgZS3Vwc8zjhjru-xbTgUa-8ljJJ-hu3HyqJtLFm9D5Rf7sBSNLQ3AfzgYUlq3mws0RLO_sTFbOoKIvW99xTaYRVXSfPD_8KUOgb4k_r72opbCo0l2O99M8TpC1Y3wjX_JsoNS449nltKhhMRLApvCzKF1cak-ZobDaIMBOAnNvaJ4vnN7Qb-Eb5aFVFzwiGDlzpLQxtxUVmO-idVGMuAs0n-ZUOKunjRZFJJQY/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Matteo Parodi