Dear Bruce,
Now, I change the standard atlas to avg152T1.nii.gz which was included in the FSL and make a mask of superior frontal gyrus (Harvard-Oxford Cortical Structural Atlas). I can map the ROI-mask to the fsaverage surface to create an fsaverage-ROI surface overlay. But when I map one subject thickness data to the fsaverage subject using the following command:
mri_surf2surf --s s12129 --trgsubject fsaverage --hemi lh --sval s12129/surf/rh.thickness --tval ~/Desktop/mask/rh.thickness.fsaverage.mgh --reshape
it said:
Reading source surface reg /Users/wangkangcheng/Desktop/dataplus_60/s12129/surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 146027 Number of value vertices = 145656
How could solve this problem?
Thank you Wang Kangcheng
you have specified the hemi as lh but passed it the rh thickness
On 6/16/14 8:44 AM, kangchengwang0808@gmail.com wrote:
Dear Bruce,
Now, I change the standard atlas to avg152T1.nii.gz which was included in the FSL and make a mask of superior frontal gyrus (Harvard-Oxford Cortical Structural Atlas). I can map the ROI-mask to the fsaverage surface to create an fsaverage-ROI surface overlay. But when I map one subject thickness data to the fsaverage subject using the following command:
/mri_surf2surf --s s12129 --trgsubject fsaverage --hemi lh --sval s12129/surf/rh.thickness --tval ~/Desktop/mask/rh.thickness.fsaverage.mgh --reshape/
it said:
/ Reading source surface reg /Users/wangkangcheng/Desktop/dataplus_60/s12129/surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 146027 Number of value vertices = 145656 / / / How could solve this problem?
Thank you Wang Kangcheng
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Wang
you can't change the atlas that way. We extract a ton of information and store it in what we call an atlas, and what we require isn't in the harvard-oxford one. What are you trying to achieve?
cheers Bruce
On Mon, 16 Jun 2014, kangchengwang0808@gmail.com wrote:
Dear Bruce,
Now, I change the standard atlas to avg152T1.nii.gz which was included in the FSL and make a mask of superior frontal gyrus (Harvard-Oxford Cortical Structural Atlas). I can map the ROI-mask to the fsaverage surface to create an fsaverage-ROI surface overlay. But when I map one subject thickness data to the fsaverage subject using the following command:
mri_surf2surf --s s12129 --trgsubject fsaverage --hemi lh --sval s12129/sur f/rh.thickness --tval ~/Desktop/mask/rh.thickness.fsaverage.mgh --reshape
it said:
Reading source surface reg /Users/wangkangcheng/Desktop/dataplus_60/s12129 /surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 146027 Number of value vertices = 145656
How could solve this problem?
Thank you Wang Kangcheng
Dear Bruce, I try to extract freesurfer cortical thickness valunes for a ROI defined in volume space (avg152T1.nii.gz). I try a lot and have extracted the values successfully now. Thank you very much. I suggest the experts can change opition "--reshape" of mri_vol2surf and mri_surf2surf into "--noreshape". If I use opition of reshapre, it always report the errors of dimension.
Thank you
Wang Kangcheng From: Bruce Fischl Date: 2014-06-16 21:04 To: kangchengwang0808@gmail.com CC: freesurfer Subject: Re: [Freesurfer] Problem of VolumeRoiCorticalThickness Hi Wang
you can't change the atlas that way. We extract a ton of information and store it in what we call an atlas, and what we require isn't in the harvard-oxford one. What are you trying to achieve?
cheers Bruce
On Mon, 16 Jun 2014, kangchengwang0808@gmail.com wrote:
Dear Bruce,
Now, I change the standard atlas to avg152T1.nii.gz which was included in the FSL and make a mask of superior frontal gyrus (Harvard-Oxford Cortical Structural Atlas). I can map the ROI-mask to the fsaverage surface to create an fsaverage-ROI surface overlay. But when I map one subject thickness data to the fsaverage subject using the following command:
mri_surf2surf --s s12129 --trgsubject fsaverage --hemi lh --sval s12129/sur f/rh.thickness --tval ~/Desktop/mask/rh.thickness.fsaverage.mgh --reshape
it said:
Reading source surface reg /Users/wangkangcheng/Desktop/dataplus_60/s12129 /surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 146027 Number of value vertices = 145656
How could solve this problem?
Thank you Wang Kangcheng
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