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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
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.billeci@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
On 2 May 2018, at 16:01, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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
On Wed, 2 May 2018, Lucia Billeci wrote:
External Email - Use CautionDear Bruce, thanks for your answer. I would like to obtain .label file for each subcortical region. I have tried the commands I reported in the previous messages but probably they are not correct. Could you please indicate me the correct way to have the .label file for subcortical regions? I am not sure if using mri_vol2label is the right way or maybe there is another strategy. 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.billeci@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.
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 On Wed, 2 May 2018, Lucia Billeci wrote:
External Email - Use Caution
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
Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.billeci@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
On 2 May 2018, at 16:01, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: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
On Wed, 2 May 2018, Lucia Billeci wrote:
External Email - Use Caution Dear Bruce, thanks for your answer. I would like to obtain .label file for each subcortical region. I have tried the commands I reported in the previous messages but probably they are not correct. Could you please indicate me the correct way to have the .label file for subcortical regions? I am not sure if using mri_vol2label is the right way or maybe there is another strategy. 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.billeci@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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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
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.billeci@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
On 2 May 2018, at 17:05, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 On Wed, 2 May 2018, Lucia Billeci wrote:
External Email - Use CautionDear 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 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.billeci@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
On 2 May 2018, at 16:01, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: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 On Wed, 2 May 2018, Lucia Billeci wrote:
External Email - Use Caution Dear Bruce, thanks for your answer. I would like to obtain .label file for each subcortical region. I have tried the commands I reported in the previous messages but probably they are not correct. Could you please indicate me the correct way to have the .label file for subcortical regions? I am not sure if using mri_vol2label is the right way or maybe there is another strategy. 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.billeci@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.
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
On 05/02/2018 12:08 PM, Lucia Billeci wrote:
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
Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.billeci@ifc.cnr.it mailto:lucia.billeci@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
On 2 May 2018, at 17:05, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
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 On Wed, 2 May 2018, Lucia Billeci wrote:
External Email - Use Caution 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 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.billeci@ifc.cnr.it mailto:lucia.billeci@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
On 2 May 2018, at 16:01, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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 On Wed, 2 May 2018, Lucia Billeci wrote:
External Email - Use Caution Dear Bruce, thanks for your answer. I would like to obtain .label file for each subcortical region. I have tried the commands I reported in the previous messages but probably they are not correct. Could you please indicate me the correct way to have the .label file for subcortical regions? I am not sure if using mri_vol2label is the right way or maybe there is another strategy. 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.billeci@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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