External Email - Use Caution Thank you. However I don’t know how to open the file .dms you sent me. I have tried several ways but unsuccessfully. Could you please tell me how to open files with this extension or maybe send me the file with another extension?
Best 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 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > On 7 May 2018, at 19:32, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > > 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><mailto: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 >>>> <mailto: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.
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