Hi all,
I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html ) I think this should be done using mri_surfcluster but I am having trouble with the actual commands. I've tried this but it doesn't seem to work:
mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi lh
the error = srcsubjid must be supplied
If I'm performing this on a group file (not individual subject), what would I even input as the subjid? Or do I have this totally wrong?
Thanks! Krista
just add "--subject fsaverage_sym"
btw, that command does not perform FDR
doug
On 01/23/2014 01:41 PM, krista kelly wrote:
Hi all,
I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html ) I think this should be done using mri_surfcluster but I am having trouble with the actual commands. I've tried this but it doesn't seem to work:
mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi lh
the error = srcsubjid must be supplied
If I'm performing this on a group file (not individual subject), what would I even input as the subjid? Or do I have this totally wrong?
Thanks! Krista
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR threshold from tksurfer and will use that as my -thmin.
One last thing, how would I view the results of mri_surfclluster in tksurfer? Would I load the ocn.mgh file? If so, I can't seem to find it.
On Thu, Jan 23, 2014 at 2:02 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
just add "--subject fsaverage_sym"
btw, that command does not perform FDR
doug
On 01/23/2014 01:41 PM, krista kelly wrote:
Hi all,
I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html ) I think this should be done using mri_surfcluster but I am having trouble with the actual commands. I've tried this but it doesn't seem to work:
mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi lh
the error = srcsubjid must be supplied
If I'm performing this on a group file (not individual subject), what would I even input as the subjid? Or do I have this totally wrong?
Thanks! Krista
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/
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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.
there are lots of output. You can create an annotation (--oannot), labels (--olab), copy the input and set nonclusters to 0 (--o), map of corrected voxel-wise significances (--vwsig), or map of cluster-wise significances (--cwsig). Of course you can get a simple table of the output too (--sum)
doug
On 01/23/2014 02:43 PM, krista kelly wrote:
Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR threshold from tksurfer and will use that as my -thmin.
One last thing, how would I view the results of mri_surfclluster in tksurfer? Would I load the ocn.mgh file? If so, I can't seem to find it.
On Thu, Jan 23, 2014 at 2:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
just add "--subject fsaverage_sym" btw, that command does not perform FDR doug On 01/23/2014 01:41 PM, krista kelly wrote: > Hi all, > > I have obtained laterality indices using xhemi analyses and would like > to use FDR instead of the mri_glmfit-sim suggested in the xhemi > instructions. I know to get the FDR threshold from tksurfer, but I > want to restrict the clusters to a certain cluster size. Based on a > previous thread ( > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html > ) I think this should be done using mri_surfcluster but I am having > trouble with the actual commands. I've tried this but it doesn't seem > to work: > > mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 > --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf > fsaverage_sym --hemi lh > > the error = srcsubjid must be supplied > > If I'm performing this on a group file (not individual subject), what > would I even input as the subjid? Or do I have this totally wrong? > > Thanks! > Krista > > > > > _______________________________________________ > 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 <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 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/ _______________________________________________ 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.
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krista kelly