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Good afternoon,
I'm new to Freesurfer; my background is resting-state fMRI using SPM. Years back, left and right cortical thickness measures were calculated for our sample of schizophrenia patients using the Desikan-Killiany atlas and were input to an SPSS spreadsheet. In an exploratory analysis of the data, I found that behavioral performance on a skills assessment was correlated with thickness of lh_rostralmiddlefrontal and lh_parstriangularis regions.
I'd like to perform a follow-up resting-state fMRI analysis, using these two surface-based parcellations ( lh_rostralmiddlefrontal and lh_parstriangularis) as seed regions and use those behavioral performance scores as a regressor. Is there a simple way to convert these two 2D-surface-based atlas measurements to masks in nifti format in 3D-volumetric space? I was doing a quick google search and came across the mri_label2vol command. Would this be helpful? Sorry for my naiveté. I appreciate your time.
Best,
Stephanie Hare Postdoctoral Fellow Neuroimaging Research Program Maryland Psychiatric Research Center
There should already be two volumes (aparc+aseg.mgz and aparc.a2009s+aseg.mgz) which you can simply convert to nifti with mri_convert file.mgz file.nii.gz
On 1/15/19 2:14 PM, Stephanie Hare wrote:
External Email - Use Caution
Good afternoon,
I'm new to Freesurfer; my background is resting-state fMRI using SPM. Years back, left and right cortical thickness measures were calculated for our sample of schizophrenia patients using the Desikan-Killiany atlas and were input to an SPSS spreadsheet. In an exploratory analysis of the data, I found that behavioral performance on a skills assessment was correlated with thickness of lh_rostralmiddlefrontal and lh_parstriangularis regions.
I'd like to perform a follow-up resting-state fMRI analysis, using these two surface-based parcellations ( lh_rostralmiddlefrontal and lh_parstriangularis) as seed regions and use those behavioral performance scores as a regressor. Is there a simple way to convert these two 2D-surface-based atlas measurements to masks in nifti format in 3D-volumetric space? I was doing a quick google search and came across the mri_label2vol command. Would this be helpful? Sorry for my naiveté. I appreciate your time.
Best,
Stephanie Hare Postdoctoral Fellow Neuroimaging Research Program Maryland Psychiatric Research Center
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dr. Greve,
Thank you for your swift reply. I will give this a try. I appreciate it. Have a nice evening.
Best,
Stephanie
On Tue, Jan 15, 2019 at 4:50 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
There should already be two volumes (aparc+aseg.mgz and aparc.a2009s+aseg.mgz) which you can simply convert to nifti with mri_convert file.mgz file.nii.gz
On 1/15/19 2:14 PM, Stephanie Hare wrote:
External Email - Use CautionGood afternoon,
I'm new to Freesurfer; my background is resting-state fMRI using SPM. Years back, left and right cortical thickness measures were calculated for our sample of schizophrenia patients using the Desikan-Killiany atlas and were input to an SPSS spreadsheet. In an exploratory analysis of the data, I found that behavioral performance on a skills assessment was correlated with thickness of lh_rostralmiddlefrontal and lh_parstriangularis regions.
I'd like to perform a follow-up resting-state fMRI analysis, using these two surface-based parcellations ( lh_rostralmiddlefrontal and lh_parstriangularis) as seed regions and use those behavioral performance scores as a regressor. Is there a simple way to convert these two 2D-surface-based atlas measurements to masks in nifti format in 3D-volumetric space? I was doing a quick google search and came across the mri_label2vol command. Would this be helpful? Sorry for my naiveté. I appreciate your time.
Best,
Stephanie Hare Postdoctoral Fellow Neuroimaging Research Program Maryland Psychiatric Research Center
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
External Email - Use Caution
Hi Doug,
I converted the aparc+aseg.mgz file for the first 4 subjects using mri_convert command as you suggested. Opening the files in an image viewer shows the full brain parcellations for each subject (see below). Is there a file (.mgz or other filetype) that specifically parcellates the lh_rostralmiddlefrontal region? I want to generate a mask of that region that can be used in 3D volumetric space for a resting-state seed (left rostral-middle-frontal) to voxel connectivity analysis. I'm worried this may be tricky given that this is a 2D-surface-based atlas measurement applied at the single subject level, and I was looking to generate and apply a single binary mask in 3D space to all 100 schizophrenia patients' normalized functional scans. Any suggestions? I appreciate your input.
Cheers,
Stephanie
[image: image.png]
On Tue, Jan 15, 2019 at 4:50 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
There should already be two volumes (aparc+aseg.mgz and aparc.a2009s+aseg.mgz) which you can simply convert to nifti with mri_convert file.mgz file.nii.gz
On 1/15/19 2:14 PM, Stephanie Hare wrote:
External Email - Use CautionGood afternoon,
I'm new to Freesurfer; my background is resting-state fMRI using SPM. Years back, left and right cortical thickness measures were calculated for our sample of schizophrenia patients using the Desikan-Killiany atlas and were input to an SPSS spreadsheet. In an exploratory analysis of the data, I found that behavioral performance on a skills assessment was correlated with thickness of lh_rostralmiddlefrontal and lh_parstriangularis regions.
I'd like to perform a follow-up resting-state fMRI analysis, using these two surface-based parcellations ( lh_rostralmiddlefrontal and lh_parstriangularis) as seed regions and use those behavioral performance scores as a regressor. Is there a simple way to convert these two 2D-surface-based atlas measurements to masks in nifti format in 3D-volumetric space? I was doing a quick google search and came across the mri_label2vol command. Would this be helpful? Sorry for my naiveté. I appreciate your time.
Best,
Stephanie Hare Postdoctoral Fellow Neuroimaging Research Program Maryland Psychiatric Research Center
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
You can extract it with mri_binarize --i aparc+aseg.mgz --match 1027 --o ctx-lh-rostralmiddlefrontal.nii.gz 1027 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt
On 1/17/19 11:31 AM, Stephanie Hare wrote:
External Email - Use Caution
Hi Doug,
I converted the aparc+aseg.mgz file for the first 4 subjects using mri_convert command as you suggested. Opening the files in an image viewer shows the full brain parcellations for each subject (see below). Is there a file (.mgz or other filetype) that specifically parcellates the lh_rostralmiddlefrontal region? I want to generate a mask of that region that can be used in 3D volumetric space for a resting-state seed (left rostral-middle-frontal) to voxel connectivity analysis. I'm worried this may be tricky given that this is a 2D-surface-based atlas measurement applied at the single subject level, and I was looking to generate and apply a single binary mask in 3D space to all 100 schizophrenia patients' normalized functional scans. Any suggestions? I appreciate your input.
Cheers,
Stephanie
image.png
On Tue, Jan 15, 2019 at 4:50 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
There should already be two volumes (aparc+aseg.mgz and aparc.a2009s+aseg.mgz) which you can simply convert to nifti with mri_convert file.mgz file.nii.gz On 1/15/19 2:14 PM, Stephanie Hare wrote: > > External Email - Use Caution > > Good afternoon, > > I'm new to Freesurfer; my background is resting-state fMRI using SPM. > Years back, left and right cortical thickness measures were calculated > for our sample of schizophrenia patients using the Desikan-Killiany > atlas and were input to an SPSS spreadsheet. In an exploratory > analysis of the data, I found that behavioral performance on a skills > assessment was correlated with thickness of lh_rostralmiddlefrontal > and lh_parstriangularis regions. > > I'd like to perform a follow-up resting-state fMRI analysis, using > these two surface-based parcellations ( lh_rostralmiddlefrontal and > lh_parstriangularis) as seed regions and use those behavioral > performance scores as a regressor. Is there a simple way to convert > these two 2D-surface-based atlas measurements to masks in nifti format > in 3D-volumetric space? I was doing a quick google search and came > across the mri_label2vol command. Would this be helpful? Sorry for > my naiveté. I appreciate your time. > > Best, > > Stephanie Hare > Postdoctoral Fellow > Neuroimaging Research Program > Maryland Psychiatric Research Center > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Stephanie Hare PhD Candidate Neuroscience Institute Georgia State University
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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Greve, Douglas N.,Ph.D. -
Stephanie Hare