I have a group of subjects, scans at time1 and time2 that have been run through the longitudinal stream. I have a group of ROIs in MNI space that I've been able to push up to fsaverage following the VolumeRoiCorticalThickness tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
Further, I've used mri_surf2surf to push the mgh file to each subject.
I'm using mri_segstats to pull out mean thickness and a few other variables. If I load the mgh into tksurfer and create a label by hand (~99% the same), I can use mris_anatomical_stats which will also output surface area. I can also use the label with mri_segstats (--slabel) to calculate the thickness, etc. and those values match the ones from mris_anatomical_stats.
Based on the input (mgh or label), I get either voxels or vertices. While not exactly the same and possibly due to creating the label by hand, the numbers are very close. However, the volume reported (GrayVol for mris_anatomical_stats, Volume_mm3 for mri_segstats) are really different between the two methods. In checking a few subjects, the volume reported for mris_anatomical_stats is usually 2-3 times larger than mri_segstats. Why is this? Which volume is correct? Is there a way to make one program calculate a volume more in line with the other? Less important, is there a way to force mri_segstats to output surface area?
Thank you for taking the time to read this
-Joel
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what is your mri_glmfit command line?
On 07/12/2017 02:32 PM, Bruss, Joel E wrote:
I have a group of subjects, scans at time1 and time2 that have been run through the longitudinal stream. I have a group of ROIs in MNI space that I've been able to push up to fsaverage following the VolumeRoiCorticalThickness tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
Further, I've used mri_surf2surf to push the mgh file to each subject.
I'm using mri_segstats to pull out mean thickness and a few other variables. If I load the mgh into tksurfer and create a label by hand (~99% the same), I can use mris_anatomical_stats which will also output surface area. I can also use the label with mri_segstats (--slabel) to calculate the thickness, etc. and those values match the ones from mris_anatomical_stats.
Based on the input (mgh or label), I get either voxels or vertices. While not exactly the same and possibly due to creating the label by hand, the numbers are very close. However, the volume reported (GrayVol for mris_anatomical_stats, Volume_mm3 for mri_segstats) are really different between the two methods. In checking a few subjects, the volume reported for mris_anatomical_stats is usually 2-3 times larger than mri_segstats. Why is this? Which volume is correct? Is there a way to make one program calculate a volume more in line with the other? Less important, is there a way to force mri_segstats to output surface area?
Thank you for taking the time to read this
-Joel
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you.
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Unless this is something invoked in the recon-all stage, I haven't run this command. Apologies if I'm misunderstanding your question. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 12, 2017 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Differences in volume between mri_segstats and mris_anatomical_stats
what is your mri_glmfit command line?
On 07/12/2017 02:32 PM, Bruss, Joel E wrote:
I have a group of subjects, scans at time1 and time2 that have been run through the longitudinal stream. I have a group of ROIs in MNI space that I've been able to push up to fsaverage following the VolumeRoiCorticalThickness tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
Further, I've used mri_surf2surf to push the mgh file to each subject.
I'm using mri_segstats to pull out mean thickness and a few other variables. If I load the mgh into tksurfer and create a label by hand (~99% the same), I can use mris_anatomical_stats which will also output surface area. I can also use the label with mri_segstats (--slabel) to calculate the thickness, etc. and those values match the ones from mris_anatomical_stats.
Based on the input (mgh or label), I get either voxels or vertices. While not exactly the same and possibly due to creating the label by hand, the numbers are very close. However, the volume reported (GrayVol for mris_anatomical_stats, Volume_mm3 for mri_segstats) are really different between the two methods. In checking a few subjects, the volume reported for mris_anatomical_stats is usually 2-3 times larger than mri_segstats. Why is this? Which volume is correct? Is there a way to make one program calculate a volume more in line with the other? Less important, is there a way to force mri_segstats to output surface area?
Thank you for taking the time to read this
-Joel
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you.
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________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________
freesurfer@nmr.mgh.harvard.edu
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Bruss, Joel E -
Douglas N Greve