External Email - Use Caution
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:
External Email - Use Caution
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 <yhuan...@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_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9ndTV9_ZapgsK_3NzhU8bMJOJY0uIz_LMPNGNff9ofQdi41lbl_z4LOot-PyyIAOkplCuie52WEoC25283K_FLApVE15eUqnyiaVpMRry06hp5_XGPLrNRm50KNv6woZtoPOOJi35Ep6MuRJkBknO4l1bQnjCysJ1851eBgeeHAOcGNtQnlEJSxyMSyXX9hlATC-lcdqDSa3tSwnR3HxF8HRuwC8fhqYKaAFcuhOJ6g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats
Best,
Yujing
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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/1dxT14leTQ7Ksa3Sgg7FIgR2pgu40NDGUaD19UIbwV0y8ZNGQXR9amganjuB0SId6OhqDBw46PFd5Kmdnh5abFjWysy25h5PMuiUsdlGN4-OdtOaTmnQp8KjOQ3KkgnacR8yIuOjlGm_CYBjKu6UjS7tU1lMh9SCP_WHSbWmBeRfMCUF5EhEj5izMkzzylPS06ADMPR4zHJTRT-iU7sNdb9l6WNGj52ISkp6Uxcw9olaXCCVM0oOyNxMjOIhvYmHzRceA9xI42kCUtW3MLFFzfQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/14wj-MDEsdpHEDgNjz6e90eBddgHiyPqXOzTlgRYOxsPbKjjYc48hxbv1EJU2aPQztS8zKU3pfbjCzfAP3OnjKig_lUF1ucsvU9K7UEQdlt5bfTFXyHDIyIZ_gn5sb9EKeP28xUaq-lLMEcMCHTed0181auYKevY8M9kljdMTLDX2wn2QKli-_VSE8PclMOMk0H4w9Fd4SXp61LoKkcxJ-nWjLZ1zx1fz64heT47JqAG799lmVUJsj9fEPXDnjOEz/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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/1nlWsXRZqUBVURSQALyhS9iySkdiXLnGAHAwkthfojjAOWIYLnCjX29voOFaLWCXdu-ChWMbFvlC3B6tl-qZSEA14gOTCHbQNwL6AJpusuOyupi_pM3Mdfiw2kITdtnvjpjBmBalErVDx2zq2-z3Z4zH4qsJd_DDD6MTPCLgA8VRqYUCKJTzmQxWQOnmDJZTCPXWOFuQjS_R_7AfNu0FTxR6g27pkddknASZC1r_6JiHgJoXm9ORFcKrqlj6vkwhP/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
<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-MDEsdpHEDgNjz6e90eBddgHiyPqXOzTlgRYOxsPbKjjYc48hxbv1EJU2aPQztS8zKU3pfbjCzfAP3OnjKig_lUF1ucsvU9K7UEQdlt5bfTFXyHDIyIZ_gn5sb9EKeP28xUaq-lLMEcMCHTed0181auYKevY8M9kljdMTLDX2wn2QKli-_VSE8PclMOMk0H4w9Fd4SXp61LoKkcxJ-nWjLZ1zx1fz64heT47JqAG799lmVUJsj9fEPXDnjOEz/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
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 Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
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.
