External Email - Use Caution 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 <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 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > On 3 May 2018, at 17:53, Douglas N. Greve <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> >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> >> >> >> > > > > 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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