External Email - Use Caution
Hi FreeSurfer developers,
I'm attempting to use FLAIR images to improve the segmentation quality of some of my subjects after successfully running recon-all -all with the T1 images. After QCing the initial results some segmentation needed improvement which is why I am trying to use the FLAIR images on the recon-all -all results with T1.
This is the command I am using: recon-all -s ${subject_id}_T1 -FLAIRpial -autorecon2 -autorecon3
but I am getting errors at the "mris_place_surface" stage.
I have also tried manually running mri_normalize first and then running recon-all with the -FLAIRpial flag (command below), but I still get the same errors. mri_normalize $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.mgz $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.norm.mgz
I have attached my recon-all.log file here in case it's of any use.
Additional info: 1- recon-all --version freesurfer-macOS-darwin_x86_64-8.0.0-20250205-0f2bd3a
2-Mac info: ProductName: macOS ProductVersion: 15.5 BuildVersion: 24F74
3- uname -a Darwin iMac.local 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:53:26 PDT 2025; root:xnu-11417.121.6~2/RELEASE_X86_64 x86_64
Also, a note that we have been able to run recon-all v6 with -FLAIR flag on the same subject on an older Mac system.
I would appreciate any insights you might have to how to improve my results using Flair images using v8 of FreeSurfer.
Thanks, Mojdeh Zamyadi, MSc (she/her)
Research Coordinator (Imaging) Centre for Youth Bipolar Disorder Centre for Addiction and Mental Health 80 Workman Way, Toronto 416-535-8501 ext. 33278
Twitter: @CYBDatCAMHhttps://secure-web.cisco.com/1YOInhbSeEqszoMsC5o-oTzaa5eOkFEeEi14Qwx4Faci68LRdSVkmnVxCWh5U5Xp19yfHBSMCAV0Yg_R76-ft7YWgbA9OC9F1hMkM_OMu_BMBPUdcmQ9wlHYQS2WEhgu0H_G1vAs2t51crm0Gp5aUx5OdnDjAfBFshGpaQKx_IKXwxd9A1trPLUUAQKewCrMIW88MYLwAKuMjD3MfJdzMxb2pIVTuoGVFmghhymqDvau9itJmngDQMYnzPufjxKEy5wP5Qv5JAfDJ2gKIL-3rQXhGui0Y7RvQpvy6J6EPZZBk2JU-N6uEQU7kj7a40IZEuMwdeGGWtgiwW6pCzrVn5w/https%3A%2F%2Ftwitter.com%2FCYBDatCAMH Website: camh.ca/CYBDhttps://secure-web.cisco.com/1-8ab9JMFlspDu1rE_5j9UF0W-Y4o0EXEfZACxBbGkZC9NrRp_Ny15ALwRReFbiSTRXxkGwS1TjyHA2mBNj49U1YItekrG4k3vhCmmagTUo63eFlSVogGhSASNUoedpoG6auMFMUR9OFxZKHMZ81_LmxydeSz206TXwv7VLSQTxF4MEuxYfFsXeQofbUb1Y1eMPPzWuTuhukGPUnASHZsIzzaHGSJl1QAToPmLXWz_IFIErySJOte0TrEn8z0YWKQay1O4ijkBrf0iqhJ_IxbvPFfdStueCPUC9xOxV91ct4TGzPsbbaCncXFbJqhNYjT0k9qpk3T48Ffx2GhU1iUpQ/https%3A%2F%2Ft.co%2FUXatZtSnyN
[cid:image001.png@01D3E3D3.C62144B0]
If you are in crisis or need urgent help: * Call the Kids Help Phone: 1-800-668-6868 or text 686868 * In Toronto, contact the Youthdale Crisis Service Line: 416-363-9990 * Go to a local hospital emergency room * Call 911
CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
AVIS DE CONFIDENTIALIT? : Ce message ?lectronique, ainsi que tout fichier qui y est joint, est reserve ? l'usage exclusif du destinataire vis? et peut contenir des renseignements confidentiels et privil?gi?s. Toute lecture, utilisation, divulgation ou distribution non autoris?e est interdite. Si vous n'?tes pas le destinataire vis?, veuillez en aviser l'exp?diteur par retour de courriel et d?truire toutes les copies du message original.
External Email - Use Caution
Dear Freesurfer is very sensitive to: 1-memory of system 2- coordinate system of FLAIR image 3- contrast equalization Check them I hope be usefull Nader
On Thu, 3 Jul 2025, 22:54 Mojdeh Zamyadi, Mojdeh.Zamyadi@camh.ca wrote:
External Email - Use CautionHi FreeSurfer developers,
I’m attempting to use FLAIR images to improve the segmentation quality of some of my subjects after successfully running recon-all –all with the T1 images. After QCing the initial results some segmentation needed improvement which is why I am trying to use the FLAIR images on the recon-all –all results with T1.
This is the command I am using: recon-all -s ${subject_id}_T1 -FLAIRpial -autorecon2 -autorecon3
but I am getting errors at the “mris_place_surface” stage.
I have also tried manually running mri_normalize first and then running recon-all with the –FLAIRpial flag (command below), but I still get the same errors. mri_normalize $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.mgz $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.norm.mgz
I have attached my recon-all.log file here in case it’s of any use.
Additional info: 1- recon-all --version
freesurfer-macOS-darwin_x86_64-8.0.0-20250205-0f2bd3a
2-Mac info: ProductName: macOS
ProductVersion: 15.5
BuildVersion: 24F74
3- uname -a
Darwin iMac.local 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:53:26 PDT 2025; root:xnu-11417.121.6~2/RELEASE_X86_64 x86_64
Also, a note that we have been able to run recon-all v6 with –FLAIR flag on the same subject on an older Mac system.
I would appreciate any insights you might have to how to improve my results using Flair images using v8 of FreeSurfer.
Thanks,
*Mojdeh Zamyadi, MSc (she/her)*
Research Coordinator (Imaging)
Centre for Youth Bipolar Disorder
Centre for Addiction and Mental Health
416-535-8501 ext. 33278
[image: cid:image001.png@01D3E3D3.C62144B0]
*If you are in crisis or need urgent help: *
· Call the Kids Help Phone: 1-800-668-6868 or text 686868
· In Toronto, contact the Youthdale Crisis Service Line: 416-363-9990
· Go to a local hospital emergency room
· Call 911
CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original. _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1nl-oFRFC9Dp913F3HmZaJRrF4prBb3oPDh2yhR6N1OzbTs... 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/15FPSaDdZaREp0olN67xGrQ-N7GfOagu4ZLxhpbio33I1P_... < https://secure-web.cisco.com/15FPSaDdZaREp0olN67xGrQ-N7GfOagu4ZLxhpbio33I1P_... .
It is not clear from the log what is happening. Is it possible that you ran out of memory?
On 7/5/2025 10:30 AM, Nader Razmara wrote:
External Email - Use Caution
Dear Freesurfer is very sensitive to: 1-memory of system 2- coordinate system of FLAIR image 3- contrast equalization Check them I hope be usefull Nader
On Thu, 3 Jul 2025, 22:54 Mojdeh Zamyadi, Mojdeh.Zamyadi@camh.ca wrote:
External Email - Use Caution Hi FreeSurfer developers, I’m attempting to use FLAIR images to improve the segmentation quality of some of my subjects after successfully running recon-all –all with the T1 images. After QCing the initial results some segmentation needed improvement which is why I am trying to use the FLAIR images on the recon-all –all results with T1. This is the command I am using: recon-all -s ${subject_id}_T1 -FLAIRpial -autorecon2 -autorecon3 but I am getting errors at the “mris_place_surface” stage. I have also tried manually running mri_normalize first and then running recon-all with the –FLAIRpial flag (command below), but I still get the same errors. mri_normalize $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.mgz $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.norm.mgz I have attached my recon-all.log file here in case it’s of any use. Additional info: 1- recon-all --version freesurfer-macOS-darwin_x86_64-8.0.0-20250205-0f2bd3a 2-Mac info: ProductName: macOS ProductVersion: 15.5 BuildVersion: 24F74 3- uname -a Darwin iMac.local 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:53:26 PDT 2025; root:xnu-11417.121.6~2/RELEASE_X86_64 x86_64 Also, a note that we have been able to run recon-all v6 with –FLAIR flag on the same subject on an older Mac system. I would appreciate any insights you might have to how to improve my results using Flair images using v8 of FreeSurfer. Thanks, *Mojdeh Zamyadi, MSc (she/her)** ** *Research Coordinator (Imaging)** Centre for Youth Bipolar Disorder Centre for Addiction and Mental Health 80 Workman Way, Toronto <https://secure-web.cisco.com/1SNq8V4joiEfxN6mEWqbM4c10its7bTk4n7sFtX7PQSFMjzRVk9Sb-McI6Fqhhy1S3Tk_NWwG07exbhLR8MVphOWNczl2grxWUBHqajRuycUNacRTVFnDMvhOfGyRollBoo0XgyHlPk8-FKytE4SprzhS4rvQvVrTPc3VWM-2tOomixvtmPXaDkJpOYX8U0gIqyYn7U03J0GrGsBj79hE6O6G5R0lB-9cKyXpQKHAnxxIBT9ACLaYxbgRdPvmFyejLMSK_R3IS5P6gDs5XBY9BOrfc1dK_XUfzUICvsl2y4eeLoGANgh60lVnDMLwuK2Y/https%3A%2F%2Fwww.google.com%2Fmaps%2Fsearch%2F80%2BWorkman%2BWay%2C%2BToronto%3Fentry%3Dgmail%26source%3Dg> 416-535-8501 ext. 33278 Twitter: @CYBDatCAMH <https://secure-web.cisco.com/1YOInhbSeEqszoMsC5o-oTzaa5eOkFEeEi14Qwx4Faci68LRdSVkmnVxCWh5U5Xp19yfHBSMCAV0Yg_R76-ft7YWgbA9OC9F1hMkM_OMu_BMBPUdcmQ9wlHYQS2WEhgu0H_G1vAs2t51crm0Gp5aUx5OdnDjAfBFshGpaQKx_IKXwxd9A1trPLUUAQKewCrMIW88MYLwAKuMjD3MfJdzMxb2pIVTuoGVFmghhymqDvau9itJmngDQMYnzPufjxKEy5wP5Qv5JAfDJ2gKIL-3rQXhGui0Y7RvQpvy6J6EPZZBk2JU-N6uEQU7kj7a40IZEuMwdeGGWtgiwW6pCzrVn5w/https%3A%2F%2Ftwitter.com%2FCYBDatCAMH> Website: camh.ca/CYBD <https://secure-web.cisco.com/1-8ab9JMFlspDu1rE_5j9UF0W-Y4o0EXEfZACxBbGkZC9NrRp_Ny15ALwRReFbiSTRXxkGwS1TjyHA2mBNj49U1YItekrG4k3vhCmmagTUo63eFlSVogGhSASNUoedpoG6auMFMUR9OFxZKHMZ81_LmxydeSz206TXwv7VLSQTxF4MEuxYfFsXeQofbUb1Y1eMPPzWuTuhukGPUnASHZsIzzaHGSJl1QAToPmLXWz_IFIErySJOte0TrEn8z0YWKQay1O4ijkBrf0iqhJ_IxbvPFfdStueCPUC9xOxV91ct4TGzPsbbaCncXFbJqhNYjT0k9qpk3T48Ffx2GhU1iUpQ/https%3A%2F%2Ft.co%2FUXatZtSnyN> cid:image001.png@01D3E3D3.C62144B0 *If you are in crisis or need urgent help: * ·Call the Kids Help Phone: 1-800-668-6868 or text 686868 ·In Toronto, contact the Youthdale Crisis Service Line: 416-363-9990 ·Go to a local hospital emergency room ·Call 911 CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original. _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ <https://secure-web.cisco.com/1nl-oFRFC9Dp913F3HmZaJRrF4prBb3oPDh2yhR6N1OzbTsdnH3tC6M6OGgsIYyxfgKXSJKUZtfYHCzEkOIUP1CsBvbTw4ySJnC5U7lFJebVG2JDqqt_Je0l1zkdmgBbZhn8gg7IzG01sJnZ_FhoMDSY7a67rjI2nz0sX9XU-gq45rVeNCq835RMqvZGyWX0Y_P86uCkykYhOwd_Se_ObHwsw-erP6-E7hN2hmDT1E8BI3sm8-bu3s0BhdOzGlnIfLT8iCRL_4uETEDgvZRaDZSySgBPrf2OsMKpVqzhXMLcGvFJSNRMK-evKCudcT4N3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F> 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://secure-web.cisco.com/15FPSaDdZaREp0olN67xGrQ-N7GfOagu4ZLxhpbio33I1P_q1m3g-a2qwZmOrNopF4eVd-ReMj-sten3Vczel_0w0rYBFZ-9FciSReDmiMFs0mM98M_M5k-a7zHOB25Dz-Cgo4v2NO34-YPOTNnRD_uSnv6VcWbYLydCPJXETuk_3TzEPB1yJmMihQquqWvxPDWEkMTwa1RoZgjLeeehJePD6R16kh6dcJyABX9MTo7du7-4CPLZ5bwO17XXPoHqPPm-q4Wk4KGeb_AnFRHa33WoezcjKRNK_xEitgzrGsSuhBxlWmWo2FN2b9ollKL15/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/15FPSaDdZaREp0olN67xGrQ-N7GfOagu4ZLxhpbio33I1P_q1m3g-a2qwZmOrNopF4eVd-ReMj-sten3Vczel_0w0rYBFZ-9FciSReDmiMFs0mM98M_M5k-a7zHOB25Dz-Cgo4v2NO34-YPOTNnRD_uSnv6VcWbYLydCPJXETuk_3TzEPB1yJmMihQquqWvxPDWEkMTwa1RoZgjLeeehJePD6R16kh6dcJyABX9MTo7du7-4CPLZ5bwO17XXPoHqPPm-q4Wk4KGeb_AnFRHa33WoezcjKRNK_xEitgzrGsSuhBxlWmWo2FN2b9ollKL15/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Mojdeh Zamyadi -
Nader Razmara