Dear all,
Given a series of fsaverage-registered rCBF maps, I am trying to extract the average rCBF value from one specific region. This region, which was a significant cluster from a volumetric (fsl) analysis, was binarized and then converted to surface.
When I run mri_segstats with the --avgwf I obtain two columns. Can you please remind me which one is the average extracted from that ROI, and what is the other column?
Thanks! Marco
mri_vol2surf --mov DMN_s1_RS1_correlates_with_ASL1_rating.gfeat/cope1.feat/cluster_mask_zstat1.nii.gz --mni152reg --hemi rh --o /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF/rh.RS1_correlates_ASL1.mgz
cd /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF
for f in `ls *.mgz` ; do
mri_segstats --seg $f --in /homes/14/marco/cluster_6/lbp/lbp_freesurfer_ASL/patients+controls/analyses/rh.lbp+ctrl.session1.asl2-asl1_projfrac-max_nopaired-diff_sm7_03mm_OCT18.mgh --avgwf "$f"_RH_nopaired_diff.txt done
nedit rh.RS1_correlates_ASL1.mgz_RH_nopaired_diff.txt &
38.2811 47.6476 40.3997 36.0856 42.6304 46.2465 44.4789 36.7066 69.2376 51.4098 66.0043 47.2098 34.5957 40.3854 36.8976 42.2028 38.2475 35.875 39.9503 37.0186 35.1582 36.6949 35.1924 38.874 43.4415 36.2505 43.3516 34.5041 58.3073 50.3295 61.8703 60.8415 61.1754 51.3476 47.9508 51.594 51.5809 48.2985 49.6545 50.974 62.9431 72.1211 54.0272 55.7234 35.0701 34.5995 37.9241 35.3844 37.2277 42.3105 38.2136 46.7896 45.0951 51.9831 45.4391 51.6242 46.2971 47.5424 44.3713 41.1725 37.4132 36.1166 36.7285 39.2947 44.0285 46.501 45.4698 50.5906 51.0392 48.2324 55.0885 50.9392 66.7224 67.7807 64.8932 68.5847 45.5101 45.6065 46.7002 45.232 40.6324 48.9768 44.3654 45.9017 39.4908 32.8936 39.5983 36.4909 55.9295 59.1527 55.6738 55.7016 44.7433 50.9412 42.6953 50.0857 42.4522 48.7366 43.5595 42.3424 43.9283 36.5026 41.9838 36.8662 39.9873 44.505 43.442 49.2243 57.6304 55.5628 53.3496 49.4215 43.2505 42.5797 43.5452 42.0694 50.4555 47.993 49.8977 49.6568 41.5077 42.8473 40.2357 42.3246 40.3846 39.1473 38.7073 41.502
______________________
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu
Hi Marco,
The columns correspond to the integer IDs in the --seg image, so assuming you passed in a binary mask the first column is mean over everything that isn't your ROI and the second column is the mean in your ROI.
Cheers, Michael
On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia marco@nmr.mgh.harvard.eduwrote:
Dear all,
Given a series of fsaverage-registered rCBF maps, I am trying to extract the average rCBF value from one specific region. This region, which was a significant cluster from a volumetric (fsl) analysis, was binarized and then converted to surface.
When I run mri_segstats with the --avgwf I obtain two columns. Can you please remind me which one is the average extracted from that ROI, and what is the other column?
Thanks! Marco
mri_vol2surf --mov
DMN_s1_RS1_correlates_with_ASL1_rating.gfeat/cope1.feat/cluster_mask_zstat1.nii.gz --mni152reg --hemi rh --o
/autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF/rh.RS1_correlates_ASL1.mgz
cd
/autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF
for f in `ls *.mgz` ; do
mri_segstats --seg $f --in
/homes/14/marco/cluster_6/lbp/lbp_freesurfer_ASL/patients+controls/analyses/rh.lbp+ctrl.session1.asl2-asl1_projfrac-max_nopaired-diff_sm7_03mm_OCT18.mgh --avgwf "$f"_RH_nopaired_diff.txt done
nedit rh.RS1_correlates_ASL1.mgz_RH_nopaired_diff.txt &
38.2811 47.6476 40.3997 36.0856 42.6304 46.2465 44.4789 36.7066 69.2376 51.4098 66.0043 47.2098 34.5957 40.3854 36.8976 42.2028 38.2475 35.875 39.9503 37.0186 35.1582 36.6949 35.1924 38.874 43.4415 36.2505 43.3516 34.5041 58.3073 50.3295 61.8703 60.8415 61.1754 51.3476 47.9508 51.594 51.5809 48.2985 49.6545 50.974 62.9431 72.1211 54.0272 55.7234 35.0701 34.5995 37.9241 35.3844 37.2277 42.3105 38.2136 46.7896 45.0951 51.9831 45.4391 51.6242 46.2971 47.5424 44.3713 41.1725 37.4132 36.1166 36.7285 39.2947 44.0285 46.501 45.4698 50.5906 51.0392 48.2324 55.0885 50.9392 66.7224 67.7807 64.8932 68.5847 45.5101 45.6065 46.7002 45.232 40.6324 48.9768 44.3654 45.9017 39.4908 32.8936 39.5983 36.4909 55.9295 59.1527 55.6738 55.7016 44.7433 50.9412 42.6953 50.0857 42.4522 48.7366 43.5595 42.3424 43.9283 36.5026 41.9838 36.8662 39.9873 44.505 43.442 49.2243 57.6304 55.5628 53.3496 49.4215 43.2505 42.5797 43.5452 42.0694 50.4555 47.993 49.8977 49.6568 41.5077 42.8473 40.2357 42.3246 40.3846 39.1473 38.7073 41.502
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu _______________________________________________ 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.
Thank you so much Michael for clarifying this.
Final, related question: is there a way to retrieve the name/paths of the files concatenated with mris_preproc to create the .mgh file mentioned below? I usually have everything logged, but was wondering if there was something like a flag for mri_info to directly find this information.
Marco
On Mar 1, 2012, at 1:18 AM, Michael Waskom wrote:
Hi Marco,
The columns correspond to the integer IDs in the --seg image, so assuming you passed in a binary mask the first column is mean over everything that isn't your ROI and the second column is the mean in your ROI.
Cheers, Michael
On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia marco@nmr.mgh.harvard.edu wrote: Dear all,
Given a series of fsaverage-registered rCBF maps, I am trying to extract the average rCBF value from one specific region. This region, which was a significant cluster from a volumetric (fsl) analysis, was binarized and then converted to surface.
When I run mri_segstats with the --avgwf I obtain two columns. Can you please remind me which one is the average extracted from that ROI, and what is the other column?
Thanks! Marco
mri_vol2surf --mov DMN_s1_RS1_correlates_with_ASL1_rating.gfeat/cope1.feat/cluster_mask_zstat1.nii.gz --mni152reg --hemi rh --o /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF/rh.RS1_correlates_ASL1.mgz
cd /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF
for f in `ls *.mgz` ; do
mri_segstats --seg $f --in /homes/14/marco/cluster_6/lbp/lbp_freesurfer_ASL/patients+controls/analyses/rh.lbp+ctrl.session1.asl2-asl1_projfrac-max_nopaired-diff_sm7_03mm_OCT18.mgh --avgwf "$f"_RH_nopaired_diff.txt done
nedit rh.RS1_correlates_ASL1.mgz_RH_nopaired_diff.txt &
38.2811 47.6476 40.3997 36.0856 42.6304 46.2465 44.4789 36.7066 69.2376 51.4098 66.0043 47.2098 34.5957 40.3854 36.8976 42.2028 38.2475 35.875 39.9503 37.0186 35.1582 36.6949 35.1924 38.874 43.4415 36.2505 43.3516 34.5041 58.3073 50.3295 61.8703 60.8415 61.1754 51.3476 47.9508 51.594 51.5809 48.2985 49.6545 50.974 62.9431 72.1211 54.0272 55.7234 35.0701 34.5995 37.9241 35.3844 37.2277 42.3105 38.2136 46.7896 45.0951 51.9831 45.4391 51.6242 46.2971 47.5424 44.3713 41.1725 37.4132 36.1166 36.7285 39.2947 44.0285 46.501 45.4698 50.5906 51.0392 48.2324 55.0885 50.9392 66.7224 67.7807 64.8932 68.5847 45.5101 45.6065 46.7002 45.232 40.6324 48.9768 44.3654 45.9017 39.4908 32.8936 39.5983 36.4909 55.9295 59.1527 55.6738 55.7016 44.7433 50.9412 42.6953 50.0857 42.4522 48.7366 43.5595 42.3424 43.9283 36.5026 41.9838 36.8662 39.9873 44.505 43.442 49.2243 57.6304 55.5628 53.3496 49.4215 43.2505 42.5797 43.5452 42.0694 50.4555 47.993 49.8977 49.6568 41.5077 42.8473 40.2357 42.3246 40.3846 39.1473 38.7073 41.502
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu _______________________________________________ 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.
______________________________
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Massachusetts General Hospital 120 Second Avenue, Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu
There should be a .log file created by mris_preproc. Is that good enough? Also, when you run mri_sestats you can add "--id 1" and it will only report the results for things inside your mask. doug
Marco Loggia, PhD wrote:
Thank you so much Michael for clarifying this.
Final, related question: is there a way to retrieve the name/paths of the files concatenated with mris_preproc to create the .mgh file mentioned below? I usually have everything logged, but was wondering if there was something like a flag for mri_info to directly find this information.
Marco
On Mar 1, 2012, at 1:18 AM, Michael Waskom wrote:
Hi Marco,
The columns correspond to the integer IDs in the --seg image, so assuming you passed in a binary mask the first column is mean over everything that isn't your ROI and the second column is the mean in your ROI.
Cheers, Michael
On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia <marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu> wrote:
Dear all, Given a series of fsaverage-registered rCBF maps, I am trying to extract the average rCBF value from one specific region. This region, which was a significant cluster from a volumetric (fsl) analysis, was binarized and then converted to surface. When I run mri_segstats with the --avgwf I obtain two columns. Can you please remind me which one is the average extracted from that ROI, and what is the other column? Thanks! Marco mri_vol2surf --mov DMN_s1_RS1_correlates_with_ASL1_rating.gfeat/cope1.feat/cluster_mask_zstat1.nii.gz --mni152reg --hemi rh --o /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF/rh.RS1_correlates_ASL1.mgz cd /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF for f in `ls *.mgz` ; do mri_segstats --seg $f --in /homes/14/marco/cluster_6/lbp/lbp_freesurfer_ASL/patients+controls/analyses/rh.lbp+ctrl.session1.asl2-asl1_projfrac-max_nopaired-diff_sm7_03mm_OCT18.mgh --avgwf "$f"_RH_nopaired_diff.txt done nedit rh.RS1_correlates_ASL1.mgz_RH_nopaired_diff.txt & 38.2811 47.6476 40.3997 36.0856 42.6304 46.2465 44.4789 36.7066 69.2376 51.4098 66.0043 47.2098 34.5957 40.3854 36.8976 42.2028 38.2475 35.875 39.9503 37.0186 35.1582 36.6949 35.1924 38.874 43.4415 36.2505 43.3516 34.5041 58.3073 50.3295 61.8703 60.8415 61.1754 51.3476 47.9508 51.594 51.5809 48.2985 49.6545 50.974 62.9431 72.1211 54.0272 55.7234 35.0701 34.5995 37.9241 35.3844 37.2277 42.3105 38.2136 46.7896 45.0951 51.9831 45.4391 51.6242 46.2971 47.5424 44.3713 41.1725 37.4132 36.1166 36.7285 39.2947 44.0285 46.501 45.4698 50.5906 51.0392 48.2324 55.0885 50.9392 66.7224 67.7807 64.8932 68.5847 45.5101 45.6065 46.7002 45.232 40.6324 48.9768 44.3654 45.9017 39.4908 32.8936 39.5983 36.4909 55.9295 59.1527 55.6738 55.7016 44.7433 50.9412 42.6953 50.0857 42.4522 48.7366 43.5595 42.3424 43.9283 36.5026 41.9838 36.8662 39.9873 44.505 43.442 49.2243 57.6304 55.5628 53.3496 49.4215 43.2505 42.5797 43.5452 42.0694 50.4555 47.993 49.8977 49.6568 41.5077 42.8473 40.2357 42.3246 40.3846 39.1473 38.7073 41.502 ______________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu <mailto:marco@nmr.mgh.harvard.edu> _______________________________________________ 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.
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Massachusetts General Hospital 120 Second Avenue, Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug, that's even more than I need! :) Good to know about the --id flag too...
Marco On Mar 1, 2012, at 10:42 AM, Douglas N Greve wrote:
There should be a .log file created by mris_preproc. Is that good enough? Also, when you run mri_sestats you can add "--id 1" and it will only report the results for things inside your mask. doug
Marco Loggia, PhD wrote:
Thank you so much Michael for clarifying this. Final, related question: is there a way to retrieve the name/paths of the files concatenated with mris_preproc to create the .mgh file mentioned below? I usually have everything logged, but was wondering if there was something like a flag for mri_info to directly find this information.
Marco
On Mar 1, 2012, at 1:18 AM, Michael Waskom wrote:
Hi Marco,
The columns correspond to the integer IDs in the --seg image, so assuming you passed in a binary mask the first column is mean over everything that isn't your ROI and the second column is the mean in your ROI.
Cheers, Michael
On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia <marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu> wrote:
Dear all,
Given a series of fsaverage-registered rCBF maps, I am trying to extract the average rCBF value from one specific region. This region, which was a significant cluster from a volumetric (fsl) analysis, was binarized and then converted to surface.
When I run mri_segstats with the --avgwf I obtain two columns. Can you please remind me which one is the average extracted from that ROI, and what is the other column?
Thanks! Marco
mri_vol2surf --mov DMN_s1_RS1_correlates_with_ASL1_rating.gfeat/cope1.feat/cluster_mask_zstat1.nii.gz --mni152reg --hemi rh --o /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF/rh.RS1_correlates_ASL1.mgz
cd /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF
for f in `ls *.mgz` ; do
mri_segstats --seg $f --in /homes/14/marco/cluster_6/lbp/lbp_freesurfer_ASL/patients+controls/analyses/rh.lbp+ctrl.session1.asl2-asl1_projfrac-max_nopaired-diff_sm7_03mm_OCT18.mgh --avgwf "$f"_RH_nopaired_diff.txt done
nedit rh.RS1_correlates_ASL1.mgz_RH_nopaired_diff.txt &
38.2811 47.6476 40.3997 36.0856 42.6304 46.2465 44.4789 36.7066 69.2376 51.4098 66.0043 47.2098 34.5957 40.3854 36.8976 42.2028 38.2475 35.875 39.9503 37.0186 35.1582 36.6949 35.1924 38.874 43.4415 36.2505 43.3516 34.5041 58.3073 50.3295 61.8703 60.8415 61.1754 51.3476 47.9508 51.594 51.5809 48.2985 49.6545 50.974 62.9431 72.1211 54.0272 55.7234 35.0701 34.5995 37.9241 35.3844 37.2277 42.3105 38.2136 46.7896 45.0951 51.9831 45.4391 51.6242 46.2971 47.5424 44.3713 41.1725 37.4132 36.1166 36.7285 39.2947 44.0285 46.501 45.4698 50.5906 51.0392 48.2324 55.0885 50.9392 66.7224 67.7807 64.8932 68.5847 45.5101 45.6065 46.7002 45.232 40.6324 48.9768 44.3654 45.9017 39.4908 32.8936 39.5983 36.4909 55.9295 59.1527 55.6738 55.7016 44.7433 50.9412 42.6953 50.0857 42.4522 48.7366 43.5595 42.3424 43.9283 36.5026 41.9838 36.8662 39.9873 44.505 43.442 49.2243 57.6304 55.5628 53.3496 49.4215 43.2505 42.5797 43.5452 42.0694 50.4555 47.993 49.8977 49.6568 41.5077 42.8473 40.2357 42.3246 40.3846 39.1473 38.7073 41.502
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu _______________________________________________ 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.
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School Massachusetts General Hospital 120 Second Avenue, Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu mailto:marco@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
______________________________
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Massachusetts General Hospital 120 Second Avenue, Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Marco Loggia -
Marco Loggia, PhD
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Michael Waskom