External Email - Use Caution
Hello, Dear FreeSurfer expert
I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all?
But the wmparc.mgz and norm.mgz are there
[image: Capture.PNG]
Could you tell me how to fix this? Thanks!
Best, Wei
I’m assuming transforms/talairach.xfm is in there? Also: what was the exact command you ran? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wei Shao wshao@research.baycrest.org Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, April 23, 2021 at 11:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampus segmentHA_T1.sh
External Email - Use Caution Hello, Dear FreeSurfer expert
I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all?
But the wmparc.mgz and norm.mgz are there
[cid:image001.png@01D73834.9E551570]
Could you tell me how to fix this? Thanks!
Best, Wei
External Email - Use Caution
Hi, E
[weishao@gra-login1 01]$ find . -name "talairach.xfm" ./mri/transforms/talairach.xfm
module load freesurfer/7.1.0
export SUBJECTS_DIR=/home/weishao/scratch/BART
segmentHA_T1.sh sub-01
Best, Wei
On Fri, Apr 23, 2021 at 11:35 AM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
I’m assuming transforms/talairach.xfm is in there?
Also: what was the exact command you ran?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1Z77TacJkkAC58QyArzEVJDV_7X8Igro89XsggKNL0YRV39s...
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wei Shao < wshao@research.baycrest.org> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, April 23, 2021 at 11:05 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Hippocampus segmentHA_T1.sh
External Email - Use Caution *Hello, Dear FreeSurfer expert
I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log
cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject.
Has the subject been procesed with recon-all?
But the wmparc.mgz and norm.mgz are there
Could you tell me how to fix this? Thanks!
Best,
Wei
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Eun7W78BTcuyipDrWGIHKg_NsRuLOs4GO-ZrOtIG85OkXl... 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 http://secure-web.cisco.com/11U8xUR8f2441jEGJ416m8uVq2qAjxEg-du5tbVs-2MtTwWq... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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.
Shouldn’t it be segmentHA_T1.sh 01 instead of segmentHA_T1.sh sub-01 ?
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wei Shao wshao@research.baycrest.org Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, April 23, 2021 at 12:04 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampus segmentHA_T1.sh
External Email - Use Caution Hi, E
[weishao@gra-login1 01]$ find . -name "talairach.xfm" ./mri/transforms/talairach.xfm
module load freesurfer/7.1.0
export SUBJECTS_DIR=/home/weishao/scratch/BART
segmentHA_T1.sh sub-01 Best, Wei
On Fri, Apr 23, 2021 at 11:35 AM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: I’m assuming transforms/talairach.xfm is in there? Also: what was the exact command you ran? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1Z77TacJkkAC58QyArzEVJDV_7X8Igro89XsggKNL0YRV39s2J3KnuYhyDYqdablT7K4waWew1NMuAm_1jfuvKuLUFGGcPObl7Lba56vs7bE-yV8BNN5sW4jWmKDYBCaTCHJKMt7IBlZicKoh235BDGiCfWiezwX2kIvAS3UlIuvd4PN_IFqc2iowh312LHnHDCQ53ea1gSk4H3Th6VAJ2NXlBvJM9qaLDKyFd02VgXiETYyw2tNFfN3h2cuLMizK/http%3A%2F%2Fwww.jeiglesias.com
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wei Shao <wshao@research.baycrest.orgmailto:wshao@research.baycrest.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, April 23, 2021 at 11:05 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampus segmentHA_T1.sh
External Email - Use Caution Hello, Dear FreeSurfer expert
I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all?
But the wmparc.mgz and norm.mgz are there
[cid:image001.png@01D73844.7B541AC0]
Could you tell me how to fix this? Thanks!
Best, Wei
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1Eun7W78BTcuyipDrWGIHKg_NsRuLOs4GO-ZrOtIG85OkXlVvZp6IvEwebF-EGHJLvKIxHkJxnrwA_ONMIv2lBS9Uv6DfnOuoxau-7DLGGrh-lPryxy4mjeHeT8fq8_CcnPObzoEJ54iSEpSV82HrEAwcsKHXm6hb3ujhqSpIhtSD03rFye6w6J7AEE8CETP8TO-ZXpupek_V0diqnrkXehUXvZXkMXJjS0U5M3QqBdE0pJGJPH56uDEDZA7K7I-9qazuodoH5LVNYDEp5fNaZA/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/11U8xUR8f2441jEGJ416m8uVq2qAjxEg-du5tbVs-2MtTwWq2aNhcq-emUFiCBDrE3ZYHesqFglrfnz6hVZWCj9jGIKgXvEEDwHTGsappvPN3pj9A6h7Fp-0PlYtKv7iJKDiXnHDmt2YNzNm34SvHO1-dNilTh85M1TgLD8X5fO2aKLcUgcP8zxmPU21jYFb-AXvxRqzdwlJ1bOC8Gm2t4mzfznlD55tbEIhtbLCjJm0KFkQDvsm8p0PnpFbmyRjiv9PNOiaCWCwT8nXMae3MQw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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.
External Email - Use Caution
HI, E
I was take the wrong directory, Sorry for the mistake.
Cheer, Wei
On Apr 23, 2021, at 1:28 PM, Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu wrote:
Shouldn’t it be segmentHA_T1.sh 01 instead of segmentHA_T1.sh sub-01 ?
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1Nx7i4KGm6MOshYnOV8FIIKnbW9fVxXk8H5ZhGy1mQM7_aYa... http://secure-web.cisco.com/19iAjCpC9PU480UGjXtraLpCYYlGzPse5r5gRi3QNJB8z34CBG6P2-8NEDc9BTmOf9nAsrHutxAiMjIrFRYYoEQ7zd5DUfDNznJqpKfpLOeChJd_R51eU9e--t3niP5Hhka7Lo0pX-fe2Nv2KNybVKmFTDsXhMSMc61QLjeLbGB19VGSQY_-n7WwsHcbxgofEBaih1GYKDl7i1eeeXcxmXiZdg14BdnP2OuUEAUR8y_jxKmQ1jvk-H9L6w4OAWybg/http%3A%2F%2Fwww.jeiglesias.com%2F
From: <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wei Shao <wshao@research.baycrest.org mailto:wshao@research.baycrest.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, April 23, 2021 at 12:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampus segmentHA_T1.sh
External Email - Use CautionHi, E
[weishao@gra-login1 01]$ find . -name "talairach.xfm" ./mri/transforms/talairach.xfm
module load freesurfer/7.1.0
export SUBJECTS_DIR=/home/weishao/scratch/BART
segmentHA_T1.sh sub-01
Best, Wei
On Fri, Apr 23, 2021 at 11:35 AM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu mailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
I’m assuming transforms/talairach.xfm is in there? Also: what was the exact command you ran? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1Nx7i4KGm6MOshYnOV8FIIKnbW9fVxXk8H5ZhGy1mQM7_aYa... http://secure-web.cisco.com/1Z77TacJkkAC58QyArzEVJDV_7X8Igro89XsggKNL0YRV39s2J3KnuYhyDYqdablT7K4waWew1NMuAm_1jfuvKuLUFGGcPObl7Lba56vs7bE-yV8BNN5sW4jWmKDYBCaTCHJKMt7IBlZicKoh235BDGiCfWiezwX2kIvAS3UlIuvd4PN_IFqc2iowh312LHnHDCQ53ea1gSk4H3Th6VAJ2NXlBvJM9qaLDKyFd02VgXiETYyw2tNFfN3h2cuLMizK/http%3A%2F%2Fwww.jeiglesias.com
From: <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wei Shao <wshao@research.baycrest.org mailto:wshao@research.baycrest.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, April 23, 2021 at 11:05 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampus segmentHA_T1.sh
External Email - Use CautionHello, Dear FreeSurfer expert
I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all?
But the wmparc.mgz and norm.mgz are there
<image001.png>
Could you tell me how to fix this? Thanks!
Best, Wei
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16U9haZBIQwQFBcRT0cXF1WactZcnPPhgGdaRUvvpaa4Fhv... https://secure-web.cisco.com/1Eun7W78BTcuyipDrWGIHKg_NsRuLOs4GO-ZrOtIG85OkXlVvZp6IvEwebF-EGHJLvKIxHkJxnrwA_ONMIv2lBS9Uv6DfnOuoxau-7DLGGrh-lPryxy4mjeHeT8fq8_CcnPObzoEJ54iSEpSV82HrEAwcsKHXm6hb3ujhqSpIhtSD03rFye6w6J7AEE8CETP8TO-ZXpupek_V0diqnrkXehUXvZXkMXJjS0U5M3QqBdE0pJGJPH56uDEDZA7K7I-9qazuodoH5LVNYDEp5fNaZA/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttp://http://secure-web.cisco.com/1mPRSAgPnLnlcGeZfx86Ky-X1J0fMXAImDTHuRims... http://secure-web.cisco.com/11U8xUR8f2441jEGJ416m8uVq2qAjxEg-du5tbVs-2MtTwWq2aNhcq-emUFiCBDrE3ZYHesqFglrfnz6hVZWCj9jGIKgXvEEDwHTGsappvPN3pj9A6h7Fp-0PlYtKv7iJKDiXnHDmt2YNzNm34SvHO1-dNilTh85M1TgLD8X5fO2aKLcUgcP8zxmPU21jYFb-AXvxRqzdwlJ1bOC8Gm2t4mzfznlD55tbEIhtbLCjJm0KFkQDvsm8p0PnpFbmyRjiv9PNOiaCWCwT8nXMae3MQw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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/16U9haZBIQwQFBcRT0cXF1WactZcnPPhgGdaRUvvpaa4Fhv... 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 http://secure-web.cisco.com/1mPRSAgPnLnlcGeZfx86Ky-X1J0fMXAImDTHuRimsuwPvQpA... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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
-
Iglesias Gonzalez, Juan E. -
Wei Shao