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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.bill...@ifc.cnr.it
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> On 2 May 2018, at 17:05, Bruce Fischl <fis...@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.bill...@ifc.cnr.it
>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>>
>> On 2 May 2018, at 16:01, Bruce Fischl <fis...@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.bill...@ifc.cnr.it
>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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