On 7 May 2018, at 19:32, Douglas N. Greve <dgreve@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.billeci@ifc.cnr.it <mailto:lucia.billeci@ifc.cnr.it>
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

On 3 May 2018, at 17:53, Douglas N. Greve <dgreve@mgh.harvard.edu<mailto:dgreve@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.billeci@ifc.cnr.it<mailto:lucia.billeci@ifc.cnr.it> <mailto:lucia.billeci@ifc.cnr.it>
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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