Dear freesurfers,
I would like to obtain the cluster size (in mm3) and coordinates of the maxima of a cortical volume comparison using mri_surfcluster.
mri_surfcluster --in $PATH/control_cronic_dones_right_volume/rh-Diff-control-cronic-Intercept-volume/sig.mgh --hemi rh --subject fsaverage --thmin 2 --thmax 7 --sign pos --surf pial --no-adjust --o ./concro --ocn ./cluster_number --olab ./grouplabel_concro --sd $SUBJ_DIR --sum ./concro_sum
Would it be correct.
Regarding the results that I obtain, I have some questions:
- Which surface do I have to load? pial, orig? - In the summary file, the cluster size is given in mm2, is it possible to obtain it in mm3 (I am analysing cortical volume)?
Thank you for your help, Yolanda
Hi Yolanda, don't use thmax (it will exclude everything with a sig>7 -- not what you want I assume). That command otherwise looks right, but it won't correct for multiple comparisons. You can run mris_anatomical_stats on the output label to give you the stats you want.
doug
Yolanda Vives wrote:
Dear freesurfers,
I would like to obtain the cluster size (in mm3) and coordinates of the maxima of a cortical volume comparison using mri_surfcluster.
mri_surfcluster --in $PATH/control_cronic_dones_right_volume/rh-Diff-control-cronic-Intercept-volume/sig.mgh --hemi rh --subject fsaverage --thmin 2 --thmax 7 --sign pos --surf pial --no-adjust --o ./concro --ocn ./cluster_number --olab ./grouplabel_concro --sd $SUBJ_DIR --sum ./concro_sum
Would it be correct.
Regarding the results that I obtain, I have some questions:
- Which surface do I have to load? pial, orig?
- In the summary file, the cluster size is given in mm2, is it
possible to obtain it in mm3 (I am analysing cortical volume)?
Thank you for your help, Yolanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Douglas for your suggestions!
If I use mris_anatomical_stats, would I perform the following procedure?
- To run "mri_label2label" to all the subjects of my comparison - To run mris_anatomical_stats. I would obtain the volume of the labels in each subject - Mean volume of all the subjects
I have tried to map the label to fsaverage and ru run mris_anatommical_stats but I have an error and I am not sure if it is correct.
Thanks again, Yolanda
2011/7/26 Douglas N Greve greve@nmr.mgh.harvard.edu
Hi Yolanda, don't use thmax (it will exclude everything with a sig>7 -- not what you want I assume). That command otherwise looks right, but it won't correct for multiple comparisons. You can run mris_anatomical_stats on the output label to give you the stats you want.
doug
Yolanda Vives wrote:
Dear freesurfers,
I would like to obtain the cluster size (in mm3) and coordinates of the maxima of a cortical volume comparison using mri_surfcluster.
mri_surfcluster --in $PATH/control_cronic_dones_** right_volume/rh-Diff-control-**cronic-Intercept-volume/sig.**mgh --hemi rh --subject fsaverage --thmin 2 --thmax 7 --sign pos --surf pial --no-adjust --o ./concro --ocn ./cluster_number --olab ./grouplabel_concro --sd $SUBJ_DIR --sum ./concro_sum
Would it be correct.
Regarding the results that I obtain, I have some questions:
- Which surface do I have to load? pial, orig?
- In the summary file, the cluster size is given in mm2, is it possible to
obtain it in mm3 (I am analysing cortical volume)?
Thank you for your help, Yolanda
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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/**compliancelinehttp://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.
Hi Yolanda,
you need to email us the screen output with the error so we can diagnose it.
cheers Bruce On Thu, 28 Jul 2011, Yolanda Vives wrote:
Thank you Douglas for your suggestions!
If I use mris_anatomical_stats, would I perform the following procedure?
- To run "mri_label2label" to all the subjects of my comparison
- To run mris_anatomical_stats. I would obtain the volume of the labels in each subject
- Mean volume of all the subjects
I have tried to map the label to fsaverage and ru run mris_anatommical_stats but I have an error and I am not sure if it is correct.
Thanks again, Yolanda
2011/7/26 Douglas N Greve greve@nmr.mgh.harvard.edu Hi Yolanda, don't use thmax (it will exclude everything with a sig>7 -- not what you want I assume). That command otherwise looks right, but it won't correct for multiple comparisons. You can run mris_anatomical_stats on the output label to give you the stats you want.
doug Yolanda Vives wrote:Dear freesurfers,
I would like to obtain the cluster size (in mm3) and coordinates of the maxima of a cortical volume comparison using mri_surfcluster.
mri_surfcluster --in $PATH/control_cronic_dones_right_volume/rh-Diff-control-cronic-Intercept-volume/sig.mgh --hemi rh --subject fsaverage --thmin 2 --thmax 7 --sign pos --surf pial --no-adjust --o ./concro --ocn ./cluster_number --olab ./grouplabel_concro --sd $SUBJ_DIR --sum ./concro_sum
Would it be correct.
Regarding the results that I obtain, I have some questions:
- Which surface do I have to load? pial, orig?
- In the summary file, the cluster size is given in mm2, is it possible to obtain it in mm3 (I am analysing cortical volume)?
Thank you for your help, Yolanda
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
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.
Hi Bruce,
That's the error:
limiting computations to label fsaverage/label/grouplabel_concro_rh-0001.label. reading volume /nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz... ERROR: cannot find /nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz mris_anatomical_stats: could not read input volume /nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz No such file or directory
cheers, yolanda
2011/7/28 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Yolanda,
you need to email us the screen output with the error so we can diagnose it.
cheers Bruce
On Thu, 28 Jul 2011, Yolanda Vives wrote:
Thank you Douglas for your suggestions!
If I use mris_anatomical_stats, would I perform the following procedure?
- To run "mri_label2label" to all the subjects of my comparison
- To run mris_anatomical_stats. I would obtain the volume of the labels in
each subject
- Mean volume of all the subjects
I have tried to map the label to fsaverage and ru run mris_anatommical_stats but I have an error and I am not sure if it is correct.
Thanks again, Yolanda
2011/7/26 Douglas N Greve greve@nmr.mgh.harvard.edu Hi Yolanda, don't use thmax (it will exclude everything with a sig>7 -- not what you want I assume). That command otherwise looks right, but it won't correct for multiple comparisons. You can run mris_anatomical_stats on the output label to give you the stats you want.
doug Yolanda Vives wrote:Dear freesurfers,
I would like to obtain the cluster size (in mm3) and coordinates of the maxima of a cortical volume comparison using mri_surfcluster.
mri_surfcluster --in $PATH/control_cronic_dones_** right_volume/rh-Diff-control-**cronic-Intercept-volume/sig.**mgh --hemi rh --subject fsaverage --thmin 2 --thmax 7 --sign pos --surf pial --no-adjust --o ./concro --ocn ./cluster_number --olab ./grouplabel_concro --sd $SUBJ_DIR --sum ./concro_sum
Would it be correct.
Regarding the results that I obtain, I have some questions:
- Which surface do I have to load? pial, orig?
- In the summary file, the cluster size is given in mm2, is it possible to
obtain it in mm3 (I am analysing cortical volume)?
Thank you for your help, Yolanda
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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/**compliancelinehttp://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.
Yolanda, don't run mris_anatomical_stats on fsaverage. You should map the label to each individual with mri_label2label, then use mris_anatomical_stats. Sorry for not being clearer eariler. doug
Yolanda Vives wrote:
Hi Bruce,
That's the error:
limiting computations to label fsaverage/label/grouplabel_concro_rh-0001.label. reading volume /nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz... ERROR: cannot find /nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz mris_anatomical_stats: could not read input volume /nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz No such file or directory
cheers, yolanda
2011/7/28 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
Hi Yolanda, you need to email us the screen output with the error so we can diagnose it. cheers Bruce On Thu, 28 Jul 2011, Yolanda Vives wrote: Thank you Douglas for your suggestions! If I use mris_anatomical_stats, would I perform the following procedure? - To run "mri_label2label" to all the subjects of my comparison - To run mris_anatomical_stats. I would obtain the volume of the labels in each subject - Mean volume of all the subjects I have tried to map the label to fsaverage and ru run mris_anatommical_stats but I have an error and I am not sure if it is correct. Thanks again, Yolanda 2011/7/26 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Hi Yolanda, don't use thmax (it will exclude everything with a sig>7 -- not what you want I assume). That command otherwise looks right, but it won't correct for multiple comparisons. You can run mris_anatomical_stats on the output label to give you the stats you want. doug Yolanda Vives wrote: Dear freesurfers, I would like to obtain the cluster size (in mm3) and coordinates of the maxima of a cortical volume comparison using mri_surfcluster. mri_surfcluster --in $PATH/control_cronic_dones_right_volume/rh-Diff-control-cronic-Intercept-volume/sig.mgh --hemi rh --subject fsaverage --thmin 2 --thmax 7 --sign pos --surf pial --no-adjust --o ./concro --ocn ./cluster_number --olab ./grouplabel_concro --sd $SUBJ_DIR --sum ./concro_sum Would it be correct. Regarding the results that I obtain, I have some questions: - Which surface do I have to load? pial, orig? - In the summary file, the cluster size is given in mm2, is it possible to obtain it in mm3 (I am analysing cortical volume)? Thank you for your help, Yolanda ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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.-- Yolanda Vives PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html
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