External Email - Use Caution        

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 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.