Re: [Freesurfer] Extract mean time series from parcellated region
Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu Sent: Monday, January 26, 2015 5:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extract mean time series from parcellated region
Works fine. thanks for the help Doug. Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, January 27, 2015 12:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region That label2vol command maps the aseg into the epi space to create test1 so it will only have 1 frame. The epi never comes into play there except as a geometry template. If you want to extract a time course from the epi, then map it to the anatomical space with that vol2vol command using the epi as the --mov, then run mri_segstats. That label2vol command is not necessary. doug On 1/27/15 12:13 PM, sabin khadka wrote: Hi doug. I now see the problem. When I run mri_info the test1.nii.gz and test2.nii.gz both have only 1 frame. But when I run # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz EPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic but I could not figure out how. I appreciate your help!! Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, January 27, 2015 10:31 AM Subject: Re: [Freesurfer] Extract mean time series from parcellated region It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu Sent: Monday, January 26, 2015 5:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail
Re: [Freesurfer] Extract mean time series from parcellated region
It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* sabin khadka sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, January 26, 2015 5:33 PM *Subject:* Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extract mean time series from parcellated region
That label2vol command maps the aseg into the epi space to create test1 so it will only have 1 frame. The epi never comes into play there except as a geometry template. If you want to extract a time course from the epi, then map it to the anatomical space with that vol2vol command using the epi as the --mov, then run mri_segstats. That label2vol command is not necessary. doug On 1/27/15 12:13 PM, sabin khadka wrote: Hi doug. I now see the problem. When I run mri_info the test1.nii.gz and test2.nii.gz both have only 1 frame. But when I run # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz EPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic but I could not figure out how. I appreciate your help!! Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* sabin khadka sabink...@yahoo.com; Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, January 27, 2015 10:31 AM *Subject:* Re: [Freesurfer] Extract mean time series from parcellated region It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* sabin khadka sabink...@yahoo.com mailto:sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, January 26, 2015 5:33 PM *Subject:* Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extract mean time series from parcellated region
Hi doug. I now see the problem. When I run mri_info the test1.nii.gz and test2.nii.gz both have only 1 frame. But when I run# mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz# mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gzEPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic but I could not figure out how. I appreciate your help!! Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, January 27, 2015 10:31 AM Subject: Re: [Freesurfer] Extract mean time series from parcellated region It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu Sent: Monday, January 26, 2015 5:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Extract mean time series from parcellated region
Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold# mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz# mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extract mean time series from parcellated region
what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
