Something like mri_segcentroid --i aseg.mgz --o centroids.dat --ctab-default
On 05/05/2018 01:06 PM, Lucia Billeci wrote: > > Sorry Douglas, > > hereafter you can find previous emails > > Regards > Lucia > > > > > > > > Dear Douglas, > thanks a lot. This can solve my problem. Could you please give my some > explanations about how to open and use the tool? > > Thanks > Regards > Lucia > > > > > mri_surfcluster only works for surfaces (that's what the "surf" in the > name means). If you want the centroid of a volume ROI use > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids > > > > > Dear Bruce, > > the ROI appears correct in freeview. However I have a problem in the > following step, i.e. obtain the centroid of the ROi. > > I used the following command: > > mri_surfcluster --in > /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel > ./tests_label/sub/lh.amygdala.label --sum > ./tests_label/sum/sum.lh.amygdala --centroid --thmin 0 --hemi lh > --subject fsaverage —nofixmni > > However it doesn’t work for subcortical label files (it works with > cortical ones). I have the following output and the command doesn’t > produce the file sum.lh.amygdala: > > thsign = abs, id = 0 > version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman > Exp $ > hemi = lh > srcid = > /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness > srcsubjid = fsaverage > srcsurf = white > srcframe = 0 > thsign = abs > thmin = 0 > thmax = -1 > fdr = -1 > minarea = 0 > xfmfile = talairach.xfm > clabelfile = ./tests_label/sub/lh.amygdala.label > clabelinv = 0 > nth = -1 > sumfile = ./tests_label/sum/sum.lh.amygdala > subjectsdir = /Applications/freesurfer/subjects > FixMNI = 0 > Loading clabel ./tests_label/sub/lh.amygdala.label. > Found 1941 points in clabel. > ------------- XFM matrix (RAS2RAS) --------------- > /Applications/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm > 1.00000 0.00000 0.00000 0.00000; > 0.00000 1.00000 0.00000 0.00000; > 0.00000 0.00000 1.00000 0.00000; > 0.00000 0.00000 0.00000 1.00000; > ---------------------------------------------------- > Reading source surface > /Applications/freesurfer/subjects/fsaverage/surf/lh.white > Done reading source surface > Computing metric properties > Loading source values > /Applications/freesurfer/bin/mri_surfcluster: line 3: 2828 Bus error: > 10 mri_surfcluster.bin "$@" > > Maybe because lh.thickness is only for cortical regions? In this case, > how can I obtain centroids of subcortical ROIs? > > Thanks > Regards > Lucia > > > > > Hi Lucia > > the first column being -1 means that it is not mapped to the surface, > so is correct in your (subcortical) case. Try loading the label as an > ROI in freeview and see if it is correct > > cheers > Bruce > > > Hi Lucia > > the first column being -1 means that it is not mapped to the surface, > so is correct in your (subcortical) case. Try loading the label as an > ROI in freeview and see if it is correct > > cheers > Bruce > > Dear Brouce, > > > thanks again. > I would like exactly how to set mri_vol2label for subcortical regions > as the way I used give me all the values of the first column equal to > -1. This is a problem when I want to obtain obtain the centroid of the > ROI using mri_surfcluster as I get an empty file. > > Hope Doug can help me. > > Thanks > Lucia > > > Hi Lucia > > can you cc the list so others can answer? You can't get a > surface-based label for a subcortical region as they aren't on (or > close) to the surrface. I think mri_vol2label is the right binary to > create a volumetric ROI for each one, but Doug will know > cheers > Bruce > > > Dear Freesurfer Experts, > > I want to use mri_vol2label to obtain labels for subcortical regions. > > I tried the following command: > > mri_vol2label --c $SUBJECTS_DIR/fsaverage/mri/aseg.mgz --id 8 --l > ./tests_label/8.label > > However I get the same vertex index for all the row, equal to -1: > > -1 -14.000 -92.000 -31.000 0.0000000000 > -1 -17.000 -92.000 -31.000 0.0000000000 > -1 -18.000 -92.000 -31.000 0.0000000000 > > This happens for all the regions I selected. > > I have also tried adding the option —surf, as you suggested in > previous posts: > > mri_vol2label --c $SUBJECTS_DIR/fsaverage/mri/aseg.mgz --id 8 --l > ./tests_label/8.label --surf fsaverage lh white > > But I have the following error message: > > ERROR: dim mismatch between surface (163842) and input (16777216) > > Could you please help me? > > Thanks a lot in advance > Best regards > Lucia Billeci > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > Dr. Lucia Billeci, PhD > Institute of Clinical Physiology (IFC) National Research Council (CNR) > via Moruzzi 1, 56124, Pisa, Italy > e-mail: lucia.bill...@ifc.cnr.it <mailto:lucia.bill...@ifc.cnr.it> > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > > > >> On 3 May 2018, at 17:53, Douglas N. Greve <dgr...@mgh.harvard.edu >> <mailto:dgr...@mgh.harvard.edu>> wrote: >> >> Please include previous emails so that I know what you are asking >> about. I get a lot of emails:) >> >> >> On 05/03/2018 05:07 AM, Lucia Billeci wrote: >>> >>> >>> Dear Douglas, >>> >>> thanks a lot. This can solve my problem. Could you please give my >>> some explanations about how to open and use the tool? >>> >>> Thanks >>> Regards >>> Lucia >>> >>> >>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>> >>> Dr. Lucia Billeci, PhD >>> Institute of Clinical Physiology (IFC) National Research Council (CNR) >>> via Moruzzi 1, 56124, Pisa, Italy >>> e-mail: lucia.bill...@ifc.cnr.it <mailto:lucia.bill...@ifc.cnr.it> >>> <mailto:lucia.bill...@ifc.cnr.it> >>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>> >>> >>> >>> >> >> >> >> 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
