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Hi I have made custom labels to use as ROIs,
I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files,
So from the lh.thickness.fwhm0.fsaverage.mgh file, would I be able to extract thickness values from this file, but just within the region covered by aparc-rh-046.label ?
Do you know of a way to do this?
Thanks Akansha
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Hi Akansha,
Can you try mri_segstats with option '--slabel subject hemi full_path_to_label' - https://secure-web.cisco.com/1_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9nd...
Best,
Yujing
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Akansha Mahesh Naraindas Sent: Thursday, June 29, 2023 3:47 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Extracting cortical thickness values for each subject using labels
External Email - Use Caution
Hi I have made custom labels to use as ROIs,
I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files,
So from the lh.thickness.fwhm0.fsaverage.mgh file, would I be able to extract thickness values from this file, but just within the region covered by aparc-rh-046.label ?
Do you know of a way to do this?
Thanks Akansha
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1dxT14leTQ7Ksa3Sgg7FIgR2pgu40NDGUaD19UIbwV0y8ZN...
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Hi Yujing
Thanks for your response, would this only provide the mean cortical thickness though? Is there a way to output cortical thickness values at each vertex in each participant?
Im also a bit confused about the segstats call, is this what you are proposing?
mri_segstats --i combatlh.thickness.fwhm0.fsaverage.mgh --slabel $SUBJECTS_DIR/fsaverage/label/DLPFC_LH.label --sum lhDLPFClabel.sum
Thanks Akansha
On 30 Jun 2023, at 15:16, Huang, Yujing YHUANG43@MGH.HARVARD.EDU wrote:
External Email - Use CautionHi Akansha,
Can you try mri_segstats with option '--slabel subject hemi full_path_to_label' - https://secure-web.cisco.com/1_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9nd...
Best,
Yujing
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Akansha Mahesh Naraindas Sent: Thursday, June 29, 2023 3:47 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Extracting cortical thickness values for each subject using labels
External Email - Use CautionHi I have made custom labels to use as ROIs,
I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files,
So from the lh.thickness.fwhm0.fsaverage.mgh file, would I be able to extract thickness values from this file, but just within the region covered by aparc-rh-046.label ?
Do you know of a way to do this?
Thanks Akansha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1dxT14leTQ7Ksa3Sgg7FIgR2pgu40NDGUaD19UIbwV0y8ZN...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1lIcSJz8HcYf7wl6z9BJu2lHEB_fHQYAFk4OjWkh2O38TiG... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1IiDW8i6LRVYf5Y2vulzMF0f6qdo77QB46Sx6tWGSK6Viog... https://secure-web.cisco.com/1IiDW8i6LRVYf5Y2vulzMF0f6qdo77QB46Sx6tWGSK6ViogENoKAgUX-AeaQk8dRwOn8s4vap459jaC773FfCLhqi7y38Q23hiG3Uv9dLs3zoK-wstKXi8rSFp_FG430MuoNHnyuKZjjcplA2swHjbTmgnMLuNeezkxf_D3pe4d0qwnn_Ps-YpQnxQkgxbvlxzBgglAejAPpUci2GK0LVuumxt9cXzqx2oLAkqnAcG3wPNc7sGXEw12dIPhVXmP-XZ_yyUvVeklKNrvdj8SdMWSSdkiWjXf8-f0Bir2VY1FA6Hlm6mKQxN9DRi5i7TWe1zD_OnqGX_-KKjis9E6ccLw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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There is not an easy way to do this. You can convert your input to ascii,eg, mri_convert --ascii+crsf input.mgz output.ascii Then find the vertex numbers that correspond to your label (visible in the .label file)
On 7/1/2023 7:06 AM, Akansha Mahesh Naraindas wrote:
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Hi Yujing
Thanks for your response, would this only provide the mean cortical thickness though? Is there a way to output cortical thickness values at each vertex in each participant?
Im also a bit confused about the segstats call, is this what you are proposing? mri_segstats --i combatlh.thickness.fwhm0.fsaverage.mgh --slabel $SUBJECTS_DIR/fsaverage/label/DLPFC_LH.label --sum lhDLPFClabel.sum
Thanks Akansha
On 30 Jun 2023, at 15:16, Huang, Yujing YHUANG43@MGH.HARVARD.EDU wrote:
External Email - Use Caution
Hi Akansha,
Can you try mri_segstats with option '--slabel subject hemi full_path_to_label' - https://secure-web.cisco.com/1_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9nd...
Best,
Yujing
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Akansha Mahesh Naraindas Sent: Thursday, June 29, 2023 3:47 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Extracting cortical thickness values for each subject using labels
External Email - Use Caution
Hi I have made custom labels to use as ROIs,
I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files,
So from the lh.thickness.fwhm0.fsaverage.mgh file, would I be able to extract thickness values from this file, but just within the region covered by aparc-rh-046.label ?
Do you know of a way to do this?
Thanks Akansha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1dxT14leTQ7Ksa3Sgg7FIgR2pgu40NDGUaD19UIbwV0y8ZN...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14wj-MDEsdpHEDgNjz6e90eBddgHiyPqXOzTlgRYOxsPbKj... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1nlWsXRZqUBVURSQALyhS9iySkdiXLnGAHAwkthfojjAOWI... https://secure-web.cisco.com/1nlWsXRZqUBVURSQALyhS9iySkdiXLnGAHAwkthfojjAOWIYLnCjX29voOFaLWCXdu-ChWMbFvlC3B6tl-qZSEA14gOTCHbQNwL6AJpusuOyupi_pM3Mdfiw2kITdtnvjpjBmBalErVDx2zq2-z3Z4zH4qsJd_DDD6MTPCLgA8VRqYUCKJTzmQxWQOnmDJZTCPXWOFuQjS_R_7AfNu0FTxR6g27pkddknASZC1r_6JiHgJoXm9ORFcKrqlj6vkwhP/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14wj-MDEsdpHEDgNjz6e90eBddgHiyPqXOzTlgRYOxsPbKj...
freesurfer@nmr.mgh.harvard.edu
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Akansha Mahesh Naraindas -
Douglas N. Greve -
Huang, Yujing