Dear Freesurfer experts,
I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage.mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder.
How can I calculate this?
Thanks for your help!
Patricia
Hi Patricia
try using the subject's rh.thickness instead (it is in subject space, as I think is your label)
cheers Bruce On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote:
Dear Freesurfer experts, I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage.mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder.
How can I calculate this?
Thanks for your help!
Patricia
Hi Bruce,
so I tried fmri/galadriel/_personal/riha_klobusiakova$ mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh but I get the same error - label point 178 has vertex number = 154391, but surface only has 140611 vertices
My labels were created by mri_surfcluster --in $SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvsPD-MCIreal/sig.mgh --subject fsaverage --hemi rh --thmin 4 --thmax 5 --thsign pos --sign pos --sum $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o /$SUBJECTS_DIR/glm/analyza/clvals --ocn /$SUBJECTS_DIR/glm/analyza/clnums --olab /$SUBJECTS_DIR/glm/analyza/cllabel
Am I missing something here? Should I create labels for every subject? I thought sig.mgh belongs to fsaverage, that's why I wanted to use rh. thickness.fwhm10.fsaverage.mgh. I wanted to create something similar to y.ocn.dat which I get after multiple comparisons correction (but for clusters significant at lower threshold).
Thanks,
Patricia
2017-08-18 2:58 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Patricia
try using the subject's rh.thickness instead (it is in subject space, as I think is your label)
cheers Bruce
On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote:
Dear Freesurfer experts,
I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage. mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder.
How can I calculate this?
Thanks for your help!
Patricia
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I'll defer to Doug on this, but it looks like your label was created on fsaverage On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote:
Hi Bruce, so I tried fmri/galadriel/_personal/riha_klobusiakova$ mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh but I get the same error - label point 178 has vertex number = 154391, but surface only has 140611 vertices
My labels were created by mri_surfcluster --in$SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvsPD-M CIreal/sig.mgh --subject fsaverage --hemi rh --thmin 4 --thmax 5 --thsign pos --sign pos --sum $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o /$SUBJECTS_DIR/glm/analyza/clvals --ocn /$SUBJECTS_DIR/glm/analyza/clnums --olab /$SUBJECTS_DIR/glm/analyza/cllabel
Am I missing something here? Should I create labels for every subject? I thought sig.mgh belongs to fsaverage, that's why I wanted to use rh.thickness.fwhm10.fsaverage.mgh. I wanted to create something similar to y.ocn.dat which I get after multiple comparisons correction (but for clusters significant at lower threshold).
Thanks,
Patricia
2017-08-18 2:58 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Patricia
try using the subject's rh.thickness instead (it is in subject space, as I think is your label) cheers Bruce On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote: Dear Freesurfer experts, I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage.mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder. How can I calculate this? Thanks for your help! Patricia
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Yes, it was. I just don't know, how to apply that on individual subjects.
Thanks!
2017-08-18 21:06 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
I'll defer to Doug on this, but it looks like your label was created on fsaverage
On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote:
Hi Bruce,
so I tried fmri/galadriel/_personal/riha_klobusiakova$ mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh but I get the same error - label point 178 has vertex number = 154391, but surface only has 140611 vertices
My labels were created by mri_surfcluster --in$SUBJECTS_DIR/glm/rh.Apgem 1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvsPD-M CIreal/sig.mgh --subject fsaverage --hemi rh --thmin 4 --thmax 5 --thsign pos --sign pos --sum $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o /$SUBJECTS_DIR/glm/analyza/clvals --ocn /$SUBJECTS_DIR/glm/analyza/clnums --olab /$SUBJECTS_DIR/glm/analyza/cllabel
Am I missing something here? Should I create labels for every subject? I thought sig.mgh belongs to fsaverage, that's why I wanted to use rh.thickness.fwhm10.fsaverage.mgh. I wanted to create something similar to y.ocn.dat which I get after multiple comparisons correction (but for clusters significant at lower threshold).
Thanks,
Patricia
2017-08-18 2:58 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Patricia
try using the subject's rh.thickness instead (it is in subject space, as I think is your label) cheers Bruce On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote: Dear Freesurfer experts, I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage.mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder. How can I calculate this? Thanks for your help! Patricia
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if you want to apply it to an individual you could map the label from fsaverage to that subject using mri_label2label On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote:
Yes, it was. I just don't know, how to apply that on individual subjects. Thanks!
2017-08-18 21:06 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: I'll defer to Doug on this, but it looks like your label was created on fsaverage On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote:
Hi Bruce, so I tried fmri/galadriel/_personal/riha_klobusiakova$ mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh but I get the same error - label point 178 has vertex number = 154391, but surface only has 140611 vertices My labels were created by mri_surfcluster--in$SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvs PD-M CIreal/sig.mgh --subject fsaverage --hemi rh --thmin 4 --thmax 5 --thsign pos --sign pos --sum $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o /$SUBJECTS_DIR/glm/analyza/clvals --ocn /$SUBJECTS_DIR/glm/analyza/clnums --olab /$SUBJECTS_DIR/glm/analyza/cllabel Am I missing something here? Should I create labels for every subject? I thought sig.mgh belongs to fsaverage, that's why I wanted to use rh.thickness.fwhm10.fsaverage.mgh. I wanted to create something similar to y.ocn.dat which I get after multiple comparisons correction (but for clusters significant at lower threshold). Thanks, Patricia 2017-08-18 2:58 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi Patricia try using the subject's rh.thickness instead (it is in subject space, as I think is your label) cheers Bruce On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote: Dear Freesurfer experts, I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage.mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder. How can I calculate this? Thanks for your help! Patricia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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OK, this works now, when I map the label on subject and use rh.thickness as an input. Don't you know why it didn't work before, when I had label from fsaverage and was trying to use rh.thickness.fwhm10.fsaverage.mgh? Aren't they both in fsaverage space?
And can I ask you one more question - how exactly are numbers in y.ocn.dat calculated (which files are used as a input)?
2017-08-18 21:14 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
if you want to apply it to an individual you could map the label from fsaverage to that subject using mri_label2label
On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote:
Yes, it was. I just don't know, how to apply that on individual subjects.
Thanks!
2017-08-18 21:06 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: I'll defer to Doug on this, but it looks like your label was created on fsaverage On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote:
Hi Bruce, so I tried fmri/galadriel/_personal/riha_klobusiakova$ mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh but I get the same error - label point 178 has vertex number = 154391, but surface only has 140611 vertices My labels were created by mri_surfcluster--in$SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvs PD-M CIreal/sig.mgh --subject fsaverage --hemi rh --thmin 4 --thmax 5 --thsign pos --sign pos --sum $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o /$SUBJECTS_DIR/glm/analyza/clvals --ocn /$SUBJECTS_DIR/glm/analyza/clnums --olab /$SUBJECTS_DIR/glm/analyza/cllabel
Am I missing something here? Should I create labels for every subject? I thought sig.mgh belongs to fsaverage, that's why I wanted to use rh.thickness.fwhm10.fsaverage.mgh. I wanted to create something similar to y.ocn.dat which I get after multiple comparisons correction (but for clusters significant at lower threshold). Thanks, Patricia 2017-08-18 2:58 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi Patricia try using the subject's rh.thickness instead (it is in subject space, as I think is your label) cheers Bruce On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote: Dear Freesurfer experts, I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage.mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder. How can I calculate this? Thanks for your help! Patricia _______________________________________________ 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.
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The numbers in that file are just indices indicating the cluster number (eg, 1=cluster1, 2=cluster2, etc). They are the output of the multiple comparisons correction, so they are gennerated from all the input
On 08/18/2017 03:28 PM, Patrícia Klobušiaková wrote:
OK, this works now, when I map the label on subject and use rh.thickness as an input. Don't you know why it didn't work before, when I had label from fsaverage and was trying to use rh.thickness.fwhm10.fsaverage.mgh? Aren't they both in fsaverage space?
And can I ask you one more question - how exactly are numbers iny.ocn.dat calculated (which files are used as a input)?
2017-08-18 21:14 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
if you want to apply it to an individual you could map the label from fsaverage to that subject using mri_label2label On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: Yes, it was. I just don't know, how to apply that on individual subjects. Thanks! 2017-08-18 21:06 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: I'll defer to Doug on this, but it looks like your label was created on fsaverage On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: Hi Bruce, so I tried fmri/galadriel/_personal/riha_klobusiakova$ mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh but I get the same error - label point 178 has vertex number = 154391, but surface only has 140611 vertices My labels were created by mri_surfcluster--in$SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvs PD-M CIreal/sig.mgh --subject fsaverage --hemi rh --thmin 4 --thmax 5 --thsign pos --sign pos --sum $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o /$SUBJECTS_DIR/glm/analyza/clvals --ocn /$SUBJECTS_DIR/glm/analyza/clnums --olab /$SUBJECTS_DIR/glm/analyza/cllabel Am I missing something here? Should I create labels for every subject? I thought sig.mgh belongs to fsaverage, that's why I wanted to use rh.thickness.fwhm10.fsaverage.mgh. I wanted to create something similar to y.ocn.dat which I get after multiple comparisons correction (but for clusters significant at lower threshold). Thanks, Patricia 2017-08-18 2:58 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Patricia try using the subject's rh.thickness instead (it is in subject space, as I think is your label) cheers Bruce On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote: Dear Freesurfer experts, I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage.mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder. How can I calculate this? Thanks for your help! Patricia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <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 <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 <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 <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.
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I meant this file: cache.th40.pos.sig.y.ocn.dat - it should contain the average value of each subject in each cluster. Are we writing about the same file?
2017-08-21 22:07 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
The numbers in that file are just indices indicating the cluster number (eg, 1=cluster1, 2=cluster2, etc). They are the output of the multiple comparisons correction, so they are gennerated from all the input
On 08/18/2017 03:28 PM, Patrícia Klobušiaková wrote:
OK, this works now, when I map the label on subject and use rh.thickness as an input. Don't you know why it didn't work before, when I had label from fsaverage and was trying to use rh.thickness.fwhm10.fsaverage.mgh? Aren't they both in fsaverage space?
And can I ask you one more question - how exactly are numbers iny.ocn.dat calculated (which files are used as a input)?
2017-08-18 21:14 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
if you want to apply it to an individual you could map the label from fsaverage to that subject using mri_label2label On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: Yes, it was. I just don't know, how to apply that on individual subjects. Thanks! 2017-08-18 21:06 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu:
I'll defer to Doug on this, but it looks like your labelwas
created on fsaverage On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: Hi Bruce, so I tried fmri/galadriel/_personal/riha_klobusiakova$ mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh but I get the same error - label point 178 has vertex number = 154391, but surface only has 140611 vertices My labels were created by mri_surfcluster--in$SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvs
PD-M CIreal/sig.mgh --subject fsaverage --hemi rh --thmin 4 --thmax 5 --thsign pos --sign pos --sum $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o /$SUBJECTS_DIR/glm/analyza/clvals --ocn /$SUBJECTS_DIR/glm/analyza/clnums --olab /$SUBJECTS_DIR/glm/analyza/cllabel Am I missing something here? Should I create labels for every subject? I thought sig.mgh belongs to fsaverage, that's why I wanted to use rh.thickness.fwhm10.fsaverage.mgh. I wanted to create something similar to y.ocn.dat which I get after multiple comparisons correction (but for clusters significant at lower threshold). Thanks, Patricia 2017-08-18 2:58 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Patricia try using the subject's rh.thickness instead (it is in subject space, as I think is your label) cheers Bruce On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote: Dear Freesurfer experts, I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage.mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder. How can I calculate this? Thanks for your help! Patricia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <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 <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>
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oh, sorry, i thought it was another file. yes, in the .dat file, the value is the mean from inside the cluster. The input is the file you passed with --y. from the help:
csdbase.y.ocn.dat - this is a summary of the input (y) over each cluster. It has a column for each cluster. Each row is a subject. The value is the average of the input (y) in each cluster. This is a simple text file.
On 08/21/2017 05:07 PM, Patrícia Klobušiaková wrote:
I meant this file: cache.th40.pos.sig.y.ocn.dat - it should contain the average value of each subject in each cluster. Are we writing about the same file?
2017-08-21 22:07 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
The numbers in that file are just indices indicating the cluster number (eg, 1=cluster1, 2=cluster2, etc). They are the output of the multiple comparisons correction, so they are gennerated from all the input On 08/18/2017 03:28 PM, Patrícia Klobušiaková wrote: > OK, this works now, when I map the label on subject and use > rh.thickness as an input. Don't you know why it didn't work before, > when I had label from fsaverage and was trying to use > rh.thickness.fwhm10.fsaverage.mgh? Aren't they both in fsaverage space? > > And can I ask you one more question - how exactly are numbers > iny.ocn.dat calculated (which files are used as a input)? > > > > 2017-08-18 21:14 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > > if you want to apply it to an individual you could map the label > from fsaverage to that subject using mri_label2label > > On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: > > Yes, it was. I just don't know, how to apply that on > individual subjects. > Thanks! > > 2017-08-18 21:06 GMT+02:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > I'll defer to Doug on this, but it looks like your label was > created on fsaverage > On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: > > Hi Bruce, > so I tried > fmri/galadriel/_personal/riha_klobusiakova$ > mris_anatomical_stats -l > $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t > $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh > but I get the same error - label point 178 has > vertex number = 154391, but > surface only has 140611 vertices > > My labels were created by > > mri_surfcluster--in$SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvs > PD-M > CIreal/sig.mgh --subject fsaverage --hemi rh --thmin > 4 --thmax 5 --thsign > pos --sign pos --sum > $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o > /$SUBJECTS_DIR/glm/analyza/clvals --ocn > /$SUBJECTS_DIR/glm/analyza/clnums > --olab /$SUBJECTS_DIR/glm/analyza/cllabel > > Am I missing something here? Should I create labels > for every subject? I > thought sig.mgh belongs to fsaverage, that's why I > wanted to > use rh.thickness.fwhm10.fsaverage.mgh. I wanted to > create something similar > to y.ocn.dat which I get after multiple comparisons > correction (but for > clusters significant at lower threshold). > > Thanks, > > Patricia > > 2017-08-18 2:58 GMT+02:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > Hi Patricia > > try using the subject's rh.thickness instead > (it is in subject > space, as I think is your label) > > cheers > Bruce > On Thu, 17 Aug 2017, Patrícia Klobušiaková > wrote: > > Dear Freesurfer experts, > I have labels representing clusters that > I created > using mri_surfcluster on > sig.mgh file using a specific threshold. > Now I want > to use these labels to > extract average thickness values for > every subject. > I tried to use > mris_anatomical_stats -l > > $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t > > > $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh > s0110B rh > to calculate it for one subject, but it > doesn't work > - I get error because > the number of vertices in subject's file > rh.thickness.fwhm10.fsaverage.mgh > doesn't match surface. I should use > fsaverage as a > subject, right? So I > tried > mris_anatomical_stats -l > > $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t > > > $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh > fsaverage rh > but then I get error, that it cannot > read fsaverage/mri/wm.mgz file. The > wm.mgz file isn't in fsaverage folder. > > How can I calculate this? > > Thanks for your help! > > Patricia > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . 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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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . 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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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. 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OK, thank you. I appreciate your help.
Patricia
2017-08-21 23:13 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
oh, sorry, i thought it was another file. yes, in the .dat file, the value is the mean from inside the cluster. The input is the file you passed with --y. from the help:
csdbase.y.ocn.dat - this is a summary of the input (y) over each cluster. It has a column for each cluster. Each row is a subject. The value is the average of the input (y) in each cluster. This is a simple text file.
On 08/21/2017 05:07 PM, Patrícia Klobušiaková wrote:
I meant this file: cache.th40.pos.sig.y.ocn.dat - it should contain the average value of each subject in each cluster. Are we writing about the same file?
2017-08-21 22:07 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
The numbers in that file are just indices indicating the cluster number (eg, 1=cluster1, 2=cluster2, etc). They are the output of themultiple
comparisons correction, so they are gennerated from all the input On 08/18/2017 03:28 PM, Patrícia Klobušiaková wrote: > OK, this works now, when I map the label on subject and use > rh.thickness as an input. Don't you know why it didn't work before, > when I had label from fsaverage and was trying to use > rh.thickness.fwhm10.fsaverage.mgh? Aren't they both in fsaverage space? > > And can I ask you one more question - how exactly are numbers > iny.ocn.dat calculated (which files are used as a input)? > > > > 2017-08-18 21:14 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > > if you want to apply it to an individual you could map thelabel
> from fsaverage to that subject using mri_label2label > > On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: > > Yes, it was. I just don't know, how to apply that on > individual subjects. > Thanks! > > 2017-08-18 21:06 GMT+02:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > I'll defer to Doug on this, but it looks like your label was > created on fsaverage > On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: > > Hi Bruce, > so I tried > fmri/galadriel/_personal/riha_klobusiakova$ > mris_anatomical_stats -l > $SUBJECTS_DIR/glm/analyza/cllabel-0001.label-t
> $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110Brh
> but I get the same error - label point 178 has > vertex number = 154391, but > surface only has 140611 vertices > > My labels were created by > > mri_surfcluster--in$SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvs
> PD-M > CIreal/sig.mgh --subject fsaverage --hemi rh --thmin > 4 --thmax 5 --thsign > pos --sign pos --sum > $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o > /$SUBJECTS_DIR/glm/analyza/clvals --ocn > /$SUBJECTS_DIR/glm/analyza/clnums > --olab /$SUBJECTS_DIR/glm/analyza/cllabel > > Am I missing something here? Should I create labels > for every subject? I > thought sig.mgh belongs to fsaverage, that's why I > wanted to > use rh.thickness.fwhm10.fsaverage.mgh. I wanted to > create something similar > to y.ocn.dat which I get after multiple comparisons > correction (but for > clusters significant at lower threshold). > > Thanks, > > Patricia > > 2017-08-18 2:58 GMT+02:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > Hi Patricia > > try using the subject's rh.thickness instead > (it is in subject > space, as I think is your label) > > cheers > Bruce > On Thu, 17 Aug 2017, PatríciaKlobušiaková
> wrote: > > Dear Freesurfer experts, > I have labels representing clusters that > I created > using mri_surfcluster on > sig.mgh file using a specific threshold. > Now I want > to use these labels to > extract average thickness valuesfor
> every subject. > I tried to use > mris_anatomical_stats -l > > $SUBJECTS_DIR/glm/analyza/cllabel-0001.label-t
> > > $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh
> s0110B rh > to calculate it for one subject, but it > doesn't work > - I get error because > the number of vertices in subject's file > rh.thickness.fwhm10.fsaverage.mgh > doesn't match surface. I should use > fsaverage as a > subject, right? So I > tried > mris_anatomical_stats -l > > $SUBJECTS_DIR/glm/analyza/cllabel-0001.label-t
> > > $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh
> fsaverage rh > but then I get error, that itcannot
> read fsaverage/mri/wm.mgz file. The > wm.mgz file isn't in fsaverage folder. > > How can I calculate this? > > Thanks for your help! > > Patricia > > > ______________________________
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> contact the sender > and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . If the e-mail was > sent to you > in error > but does not contain patient information, please contactthe
> sender > and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Patrícia Klobušiaková