Hi,
I'm trying to get some cortical thickness volumes for an ROI that I have (I'm pretty much following the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness verbatim), but for some of my subjects I'm getting errors that look like this when I run mdi_segstats:
ERROR: dimension mismatch between input volume and seg input 1 1 145283 seg 145283 1 1
Does anyone have any thoughts on how to trouble-shoot this one?
Thanks!
Hi Kari
I think that's not a real error. They are both surface overlays, just with the nvertices dimension in different slots. You could load one of them into matlab and use reshape to make it the same dimensions as the other, then write it out
cheers Bruce
On Fri, 20 May 2016, Kari Parsons wrote:
Hi,
I'm trying to get some cortical thickness volumes for an ROI that I have (I'm pretty much following the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness verbatim), but for some of my subjects I'm getting errors that look like this when I run mdi_segstats:ERROR: dimension mismatch between input volume and seg input 1 1 145283 seg 145283 1 1
Does anyone have any thoughts on how to trouble-shoot this one?Thanks! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try it without the --reshape option in mri_surf2surf
On 05/20/2016 05:51 PM, Kari Parsons wrote:
Hi,
I'm trying to get some cortical thickness volumes for an ROI that I have (I'm pretty much following the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness verbatim), but for some of my subjects I'm getting errors that look like this when I run mdi_segstats:ERROR: dimension mismatch between input volume and seg input 1 1 145283 seg 145283 1 1
Does anyone have any thoughts on how to trouble-shoot this one?Thanks! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This worked! Thanks very much for your help!
On 2016-05-23, at 11:25 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Try it without the --reshape option in mri_surf2surf
On 05/20/2016 05:51 PM, Kari Parsons wrote:
Hi,
I'm trying to get some cortical thickness volumes for an ROI that I have (I'm pretty much following the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness verbatim), but for some of my subjects I'm getting errors that look like this when I run mdi_segstats:ERROR: dimension mismatch between input volume and seg input 1 1 145283 seg 145283 1 1
Does anyone have any thoughts on how to trouble-shoot this one?Thanks! _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Hi,
I'm using ROI masks (spectroscopy voxels) to get cortical thickness values. I'm pretty much following the tutorial online ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks like Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and I'm getting that as the maximum cortical thickness for a fair number of subject's ROI. I'd really like to hear thoughts on this: if it might be indicative of some error happening and if my mean or range cortical thickness is going to be thrown off by it?
Thanks for your help, Kari
Hi Kari
the average thickness in some ROIs is 5mm??? Like which ones? That certainly seems like something is wrong. Do the surfaces look accurate? What were the parameters/resolution/sequence of the data you gave to recon-all?
cheers Bruce
On Fri, 3 Jun 2016, Kari Parsons wrote:
Hi,
I'm using ROI masks (spectroscopy voxels) to get cortical thickness values. I'm pretty much following the tutorial online ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks like Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and I'm getting that as the maximum cortical thickness for a fair number of subject's ROI. I'd really like to hear thoughts on this: if it might be indicative of some error happening and if my mean or range cortical thickness is going to be thrown off by it?Thanks for your help, Kari
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Yes, I agree it doesn't seem right. They're LAG and ACG (I'm using spectroscopy voxels as my ROIs). The surfaces look reasonable when I'm running through the suggested steps on the freesurfer website for getting the surface thickness when using an roi as a mask, but when I look at them in freeviewer the voxels are definitely not in the correct spot (they're pretty far off).
The acquisition parameters for the scan were pretty standard (BRAVO sequence with 1 mm^3 isotropic voxels). The steps that I ran through with the spectroscopy voxel were:
tkmedit -f ${subj_T1} -overlay ${spectroscopy_voxel_mask} -fthresh 0.5
mri_vol2surf --mov ${spectroscopy_voxel_mask} --hemi lh --out lh.${subj_number}.ACG.mgh
cd ${subj_number}/surf
tksurfer ${subj_number} lh inflated -overlay lh.${subj_number}.ACG.mgh -fthresh 0.5
mri_surf2surf --s ${subj_number} --trgsubject ${subj_number} --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape
mri_segstats --seg lh.${subj_number}.ACG.mgh --in ${subj_number}/surf/lh.thickness.fsaverage.mgh --sum segstats-${subj_number}.txt
Thanks very much, Kari
On 2016-06-02, at 6:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Kari
the average thickness in some ROIs is 5mm??? Like which ones? That certainly seems like something is wrong. Do the surfaces look accurate? What were the parameters/resolution/sequence of the data you gave to recon-all?
cheers Bruce
On Fri, 3 Jun 2016, Kari Parsons wrote:
Hi,
I'm using ROI masks (spectroscopy voxels) to get cortical thickness values. I'm pretty much following the tutorial online ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks like Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and I'm getting that as the maximum cortical thickness for a fair number of subject's ROI. I'd really like to hear thoughts on this: if it might be indicative of some error happening and if my mean or range cortical thickness is going to be thrown off by it?
Thanks for your help, Kari
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Kari
what do you mean when you say "when I look at them in freeviewer the voxels are definitely not in the correct spot". Do you mean the spectroscopy voxels?
cheers Bruce
On Fri, 22 Jul 2016, Kari Parsons wrote:
Hi Bruce,
Yes, I agree it doesn't seem right. They're LAG and ACG (I'm usingspectroscopy voxels as my ROIs). The surfaces look reasonable when I'm running through the suggested steps on the freesurfer website for getting the surface thickness when using an roi as a mask, but when I look at them in freeviewer the voxels are definitely not in the correct spot (they're pretty far off).
The acquisition parameters for the scan were pretty standard (BRAVOsequence with 1 mm^3 isotropic voxels). The steps that I ran through with the spectroscopy voxel were:
tkmedit -f ${subj_T1} -overlay ${spectroscopy_voxel_mask} -fthresh 0.5
mri_vol2surf --mov ${spectroscopy_voxel_mask} --hemi lh --out lh.${subj_number}.ACG.mgh
cd ${subj_number}/surf
tksurfer ${subj_number} lh inflated -overlay lh.${subj_number}.ACG.mgh -fthresh 0.5
mri_surf2surf --s ${subj_number} --trgsubject ${subj_number} --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape
mri_segstats --seg lh.${subj_number}.ACG.mgh --in ${subj_number}/surf/lh.thickness.fsaverage.mgh --sum segstats-${subj_number}.txt
Thanks very much, Kari
On 2016-06-02, at 6:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Kari
the average thickness in some ROIs is 5mm??? Like which ones? That certainly seems like something is wrong. Do the surfaces look accurate? What were the parameters/resolution/sequence of the data you gave to recon-all?
cheers Bruce
On Fri, 3 Jun 2016, Kari Parsons wrote:
Hi,
I'm using ROI masks (spectroscopy voxels) to get cortical thickness values. I'm pretty much following the tutorial online ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks like Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and I'm getting that as the maximum cortical thickness for a fair number of subject's ROI. I'd really like to hear thoughts on this: if it might be indicative of some error happening and if my mean or range cortical thickness is going to be thrown off by it?
Thanks for your help, Kari
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Kari Parsons