Did I send a .dms file? It should just be a binary
On 05/08/2018 04:25 AM, Lucia Billeci wrote: > > > 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 <mailto:lucia.bill...@ifc.cnr.it> > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > > > >> On 7 May 2018, at 19:32, Douglas N. Greve <dgr...@mgh.harvard.edu >> <mailto: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>> 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> >>>>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
