External Email - Use Caution
Dear Experts, I am looking for a way to extract information on the location (xyz coordinates in MNI space) of a vertex with the lowest thickness value within an ROI (label) for a group of subjects. I have previously ran recon-all and qcache on the data.
Any insights will be welcome!
Thank you in advance and kind regards, Olga Kepinska
-- Olga Kepinska, PhD she/her Postdoctoral Researcher Brain and Language Lab (http://secure-web.cisco.com/1sChCMMb6dwvPKcri0GopC5Le8_9OomfgYJzxDh8yt_dSgyu...) University of Vienna @olgakepinska
Once you have the vertex number, you can get the MNI coordinate through some combination of operations shown on this page https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems Getting the minimum vertex is a little trickier. I would probably load the thickness into matlab, eg, thickness = MRIread('lh.thickness.mgz'); % you can convert it to mgz with mri_convert lh.thickness lh.thickness.mgz Then load in the annot, eg, [vertices label ctab] = read_annotation('lh.aparc.annot') Then finding the minimum vertex in your ROI
On 9/12/2022 12:52 PM, Olga Kepinska wrote:
External Email - Use Caution
Dear Experts, I am looking for a way to extract information on the location (xyz coordinates in MNI space) of a vertex with the lowest thickness value within an ROI (label) for a group of subjects. I have previously ran recon-all and qcache on the data.
Any insights will be welcome!
Thank you in advance and kind regards, Olga Kepinska
-- Olga Kepinska, PhD /she/her/ Postdoctoral Researcher Brain and Language Lab (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://www.brainandlanguagelab.org http://secure-web.cisco.com/1sChCMMb6dwvPKcri0GopC5Le8_9OomfgYJzxDh8yt_dSgyuAXWuDiSBoJPntQh-1e0-TPS4pnvOl84OW9Kc0ACVkYYyqqu2j5GrGXM7aOf-rgAqg8NnFSBlcqeiqJnPjWtD5uKYGMfT9cWe3z54XpJjDv4L7TjOSaTBnZu7iSI3m84sNhfUn6rzgeKasScJAR8C5hXligzFehYsppEwBAQTjZ-q9CBuS6gCQDTV1aFW89bcihvh6FDboNwG-AxrkZOGnKbwuAHr9fR0qrm09IA4g3LC8RGJLpEkPkG8kg2uh8HvYqctW_q1sQCHSBe9k/http%3A%2F%2Fwww.brainandlanguagelab.org) University of Vienna @olgakepinska
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you, Douglas! Kind regards, Olga
On Sep 13, 2022, at 3:41 PM, Douglas N. Greve dgreve@MGH.HARVARD.EDU wrote:
Once you have the vertex number, you can get the MNI coordinate through some combination of operations shown on this page https://secure-web.cisco.com/1AMLX7FQQXCeAZwrhk6bLLv0EQxgK-Ds-appWhDX7MO7oFD... https://secure-web.cisco.com/1AMLX7FQQXCeAZwrhk6bLLv0EQxgK-Ds-appWhDX7MO7oFDpkHrcAthdt6FRiOVvze-ZyYLBDKS8vMpuCQEcpRFXspnR2A6tA2B-iYHQXqWvNzYLqNmHTkNnzyfXBetbFS1phkMn_wtOS8T-uRutznm7qV41e1PuT4R92jln2NscpCg8mfaxUV7haygQZDwokS-b8gSB0jTnHt1V0bGtlDulIAMHdmdzCKhIx8nisrmRlXboY5f44Psxnl2VTg0-Vyb97r0R0GTSSqoDEOWerG3uvB1gYPQoiHP16hQqTOfnLfNE9718fBBuIroJ7PjMh/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCoordinateSystems Getting the minimum vertex is a little trickier. I would probably load the thickness into matlab, eg, thickness = MRIread('lh.thickness.mgz'); % you can convert it to mgz with mri_convert lh.thickness lh.thickness.mgz Then load in the annot, eg, [vertices label ctab] = read_annotation('lh.aparc.annot') Then finding the minimum vertex in your ROI
On 9/12/2022 12:52 PM, Olga Kepinska wrote:
External Email - Use CautionDear Experts, I am looking for a way to extract information on the location (xyz coordinates in MNI space) of a vertex with the lowest thickness value within an ROI (label) for a group of subjects. I have previously ran recon-all and qcache on the data.
Any insights will be welcome!
Thank you in advance and kind regards, Olga Kepinska
-- Olga Kepinska, PhD >> she/her Postdoctoral Researcher Brain and Language Lab (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1-e84HxZagABG5hLK4HsHXbqdaz8WBkf60Y-G3rhr2-mQehJ... http://secure-web.cisco.com/1sChCMMb6dwvPKcri0GopC5Le8_9OomfgYJzxDh8yt_dSgyuAXWuDiSBoJPntQh-1e0-TPS4pnvOl84OW9Kc0ACVkYYyqqu2j5GrGXM7aOf-rgAqg8NnFSBlcqeiqJnPjWtD5uKYGMfT9cWe3z54XpJjDv4L7TjOSaTBnZu7iSI3m84sNhfUn6rzgeKasScJAR8C5hXligzFehYsppEwBAQTjZ-q9CBuS6gCQDTV1aFW89bcihvh6FDboNwG-AxrkZOGnKbwuAHr9fR0qrm09IA4g3LC8RGJLpEkPkG8kg2uh8HvYqctW_q1sQCHSBe9k/http%3A%2F%2Fwww.brainandlanguagelab.org) University of Vienna @olgakepinska
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1DwUOU9u07NOkc_bTbz_Pha7f4t_cCOiFDccJ3vVTaIQt1J... https://secure-web.cisco.com/1DwUOU9u07NOkc_bTbz_Pha7f4t_cCOiFDccJ3vVTaIQt1JLxoQvrhAAG1MM-kqxM9ZKv6FHChKsUbhMY9iIV-2JvQkdv8D9Jcs4ZiXIE0O6XGiBDPJXpWbWC4JlmEmzTa2sEFpCxl2AJDAXEmNn2CkJvXGwnJFRYG8HWkUypY7h19uRQ0WoFxsM9NkBzi8GC7gxpT0BMfHt40VntI9FMYn7T-i-CKSFnPT_e3xXWznpQ6E-dp8-zwq4T-irpiaeYrGAV4H6Bg0lMfj3ujoxQLmIN9NJWNbBSqDrVpCKtMTA53yeu3cszAY3tmz3J2wo-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1DwUOU9u07NOkc_bTbz_Pha7f4t_cCOiFDccJ3vVTaIQt1J... 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/11QhbAdiBJ8HcdWBlABbzMPc3LB-au7iXPHjf2OPHcbmPA7... https://secure-web.cisco.com/11QhbAdiBJ8HcdWBlABbzMPc3LB-au7iXPHjf2OPHcbmPA78DcnYHdPT9RiCsJvmq7xLzqYee9iUHFHAC3A8RDM-S1w7uw8FVV0AofEABJ4vhjdh5Tw3VzWrlWW8_c_c0C0XVwzQY6rZmKeEg-T5ycPSHA2u_pA8OHj5as8m5lqjoTlHVIS5PmTt4aj6Uf5tMbzlCQvIaCr8KNufU7tPZ7_mygvrE7BugLCYCnxzBQYfFYw4wEPGU76zNsYjwIjsjN8ng2ZRXv-T8fG05vhz5VkO4FKrTKQZcYyKK5eKrdqEkhHEFKShU14unwSpK95Pl/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@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Olga Kepinska