Re: [Freesurfer] mri_vol2surf wrong hemisphere

2017-12-07 Thread Defenderfer, Matthew K 
Hi Doug,


FSLView gives a label of L and R and the parcels on the LH in fslview match the 
LH parcels in their included Excel spreadsheet. That's really all the 
verification I have for it right now. It's possible they switched the 
hemispheres when they made the original parcellation volume before making the 
excel sheet, but I don't know how likely that is. Is there anything I can do to 
help out with this?


-Matt


Matthew K. Defenderfer B.S. | Graduate Research Assistant

Graduate Biomedical Sciences | Neuroscience

UAB | The University of Alabama at Birmingham

Laboratory of Kristina Visscher, PhD

Department of Neurobiology

CIRC 111 | C: (865) 805-6389



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve 
<gr...@nmr.mgh.harvard.edu>
Sent: Monday, December 4, 2017 11:46:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2surf wrong hemisphere

How do you know what is right and left in the volume?


On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote:
>
> Hi,
>
> I have a strange issue I can't figure out. I am currently trying to
> use the parcellation from Gordon et al. 2014
> (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs
> for the frontoparietal network. They provided a volume of the
> parcellation in MNI152 space for public use. I took this volume and
> applied the mri_vol2surf command to it to create 2 overlays of the
> parcels, 1 for each hemisphere. The code was:
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage
> --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage
> --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh
>
> The code ran, but the LH parcels in the volume were transferred to the
> RH on the surface and vice versa. This is a problem since the
> parcellation is not symmetric across hemispheres.This is not a problem
> with the volume either as I looked at it overlayed with the MNI152
> brain in fslview and saw that the parcels were on the correct
> hemisphere. Another problem is that 1 of the frontoparietal parcels,
> number 24, was not found on the surface of either hemisphere after
> turning it to a surface. I don't know why this would be the case since
> there are all cortical parcels.
>
> I have also tried this with a volume ROI that is only located on the
> left hemisphere. After running essentially the same vol2surf command
> as above, the ROI only appeared on the RH surface. I am using
> mri_vol2surf from Freesurfer v6.0.0
>
>
> Any help would be greatly appreciated. Thank you!
>
> Best,
> Matthew Defenderfer
>
>
> *Matthew K. Defenderfer B.S. | Graduate Research Assistant*
>
> Graduate Biomedical Sciences|Neuroscience
>
> UAB | The University of Alabama at Birmingham
>
> Laboratory of Kristina Visscher, PhD
>
> Department of Neurobiology
>
> CIRC 111 | C: (865) 805-6389
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_vol2surf wrong hemisphere

2017-12-04 Thread Douglas N Greve 
How do you know what is right and left in the volume?


On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote:
>
> Hi,
>
> I have a strange issue I can't figure out. I am currently trying to 
> use the parcellation from Gordon et al. 2014 
> (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs 
> for the frontoparietal network. They provided a volume of the 
> parcellation in MNI152 space for public use. I took this volume and 
> applied the mri_vol2surf command to it to create 2 overlays of the 
> parcels, 1 for each hemisphere. The code was:
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage 
> --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage 
> --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh
>
> The code ran, but the LH parcels in the volume were transferred to the 
> RH on the surface and vice versa. This is a problem since the 
> parcellation is not symmetric across hemispheres.This is not a problem 
> with the volume either as I looked at it overlayed with the MNI152 
> brain in fslview and saw that the parcels were on the correct 
> hemisphere. Another problem is that 1 of the frontoparietal parcels, 
> number 24, was not found on the surface of either hemisphere after 
> turning it to a surface. I don't know why this would be the case since 
> there are all cortical parcels.
>
> I have also tried this with a volume ROI that is only located on the 
> left hemisphere. After running essentially the same vol2surf command 
> as above, the ROI only appeared on the RH surface. I am using 
> mri_vol2surf from Freesurfer v6.0.0
>
>
> Any help would be greatly appreciated. Thank you!
>
> Best,
> Matthew Defenderfer
>
>
> *Matthew K. Defenderfer B.S. | Graduate Research Assistant*
>
> Graduate Biomedical Sciences|Neuroscience
>
> UAB | The University of Alabama at Birmingham
>
> Laboratory of Kristina Visscher, PhD
>
> Department of Neurobiology
>
> CIRC 111 | C: (865) 805-6389
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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
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dispose of the e-mail.

[Freesurfer] mri_vol2surf wrong hemisphere

2017-12-01 Thread Defenderfer, Matthew K 
Hi,

I have a strange issue I can't figure out. I am currently trying to use the 
parcellation from Gordon et al. 2014 
(http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs for the 
frontoparietal network. They provided a volume of the parcellation in MNI152 
space for public use. I took this volume and applied the mri_vol2surf command 
to it to create 2 overlays of the parcels, 1 for each hemisphere. The code was:

mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o 
lh.Parcels_fsaverage_111.mgh --hemi lh

mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o 
rh.Parcels_fsaverage_111.mgh --hemi rh

The code ran, but the LH parcels in the volume were transferred to the RH on 
the surface and vice versa. This is a problem since the parcellation is not 
symmetric across hemispheres.This is not a problem with the volume either as I 
looked at it overlayed with the MNI152 brain in fslview and saw that the 
parcels were on the correct hemisphere. Another problem is that 1 of the 
frontoparietal parcels, number 24, was not found on the surface of either 
hemisphere after turning it to a surface. I don't know why this would be the 
case since there are all cortical parcels.

I have also tried this with a volume ROI that is only located on the left 
hemisphere. After running essentially the same vol2surf command as above, the 
ROI only appeared on the RH surface. I am using mri_vol2surf from Freesurfer 
v6.0.0


Any help would be greatly appreciated. Thank you!

Best,
Matthew Defenderfer


Matthew K. Defenderfer B.S. | Graduate Research Assistant

Graduate Biomedical Sciences | Neuroscience

UAB | The University of Alabama at Birmingham

Laboratory of Kristina Visscher, PhD

Department of Neurobiology

CIRC 111 | C: (865) 805-6389

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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mri_vol2surf wrong hemisphere

2017-12-01 Thread Defenderfer, Matthew K 
Hi,

I have a strange issue I can't figure out. I am currently trying to use the 
parcellation from Gordon et al. 2014 (download link 
here) to create ROIs for 
the frontoparietal network. They provided a volume of the parcellation in 
MNI152 space for public use. I took this volume and applied the mri_vol2surf 
command to it to create 2 overlays of the parcels, 1 for each hemisphere. The 
code was:

mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o 
lh.Parcels_fsaverage_111.mgh --hemi lh

mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o 
rh.Parcels_fsaverage_111.mgh --hemi rh

The code ran, but the LH parcels in the volume were transferred to the RH on 
the surface and vice versa. This is a problem since the parcellation is not 
symmetric across hemispheres.This is not a problem with the volume either as I 
looked at it overlayed with the MNI152 brain in fslview and saw that the 
parcels were on the correct hemisphere. Another problem is that 1 of the 
frontoparietal parcels, number 24, was not found on the surface of either 
hemisphere after turning it to a surface. I don't know why this would be the 
case since there are all cortical parcels.

I have also tried this with a volume ROI that is only located on the left 
hemisphere. After running essentially the same vol2surf command as above, the 
ROI only appeared on the RH surface. I am using mri_vol2surf from Freesurfer 
v6.0.0


Any help would be greatly appreciated. Thank you!

Best,
Matthew Defenderfer



Matthew K. Defenderfer B.S. | Graduate Research Assistant

Graduate Biomedical Sciences | Neuroscience

UAB | The University of Alabama at Birmingham

Laboratory of Kristina Visscher, PhD

Department of Neurobiology

CIRC 111 | C: (865) 805-6389

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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.