[Freesurfer] time series data from FSFAST
Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. 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] time series data from FSFAST
Thanks Doug. I am now able to get average time series from cortical ROIs. I usedmri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txtHow would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)?I tried doingmri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txtbut it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 9, 2015 1:24 PM Subject: Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] time series data from FSFAST
Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] time series data from FSFAST
On 2/9/15 3:16 PM, sabin khadka wrote: Thanks Doug. I am now able to get average time series from cortical ROIs. I used mri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt That's right, but I would use the unsmoothed data since smoothing will cause activity to spill-over between regions. How would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)? I tried doing mri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt but it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Use fsaverage/mri.2mm/aseg.mgz doug Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, February 9, 2015 1:24 PM *Subject:* Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. 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 ___ 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 ___ 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] time series data from FSFAST
Hi Doug- Works fine. I appreciate your help. Related but different question: Would you help me understand how the QA value(0-1)while checking registration using following command is calculated. tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 9, 2015 3:32 PM Subject: Re: [Freesurfer] time series data from FSFAST On 2/9/15 3:16 PM, sabin khadka wrote: Thanks Doug. I am now able to get average time series from cortical ROIs. I used mri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt That's right, but I would use the unsmoothed data since smoothing will cause activity to spill-over between regions. How would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)? I tried doing mri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt but it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Use fsaverage/mri.2mm/aseg.mgz doug Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 9, 2015 1:24 PM Subject: Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 ___ 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] time series data from FSFAST
That is the cost of the registration. You can look in Greve Fischl 2009 to see how it is computed. doug On 2/9/15 3:45 PM, sabin khadka wrote: Hi Doug- Works fine. I appreciate your help. Related but different question: Would you help me understand how the QA value(0-1)while checking registration using following command is calculated. tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, February 9, 2015 3:32 PM *Subject:* Re: [Freesurfer] time series data from FSFAST On 2/9/15 3:16 PM, sabin khadka wrote: Thanks Doug. I am now able to get average time series from cortical ROIs. I used mri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt That's right, but I would use the unsmoothed data since smoothing will cause activity to spill-over between regions. How would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)? I tried doing mri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt but it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Use fsaverage/mri.2mm/aseg.mgz doug Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, February 9, 2015 1:24 PM *Subject:* Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. 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 ___ 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 ___ 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 ___ 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.
