External Email - Use Caution
---------- Forwarded message --------- From: Wei Shao wshao@research.baycrest.org Date: Thu, Mar 11, 2021 at 11:38 AM Subject: Re: [Freesurfer] Hippocampal subfield segmentation To: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu
Hi, Freesurfer experts
I have tried different T1 and T2 inputs for recon-all and subfield segmentation. As you can see, the left is the axial_T1 scan for recon-all and reoriented T2 scan for subfield segmentation. The right is the sagittal_T1 for recon-all + original_T2 for subfield segmentation.
The automated segmentation looks better after reorientation but It seems like there are more “wrinkle” after the re-orientation
I also check the original T2 scan, there are a few "Wrinkles" but overall it is good (no wrinkles in hippocampus areas, I guess).
Could you tell me how to erase these “wrinkles”,(if possible)?
Best, Wei
[image: 11958_L.PNG][image: BAY11958_R.PNG]
On Tue, Mar 9, 2021 at 2:36 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Hi again,
I think the problem is that the T1 and T2 were in different RAS spaces (maybe a problem when converting the DICOMS?)
Can you please try again, but using this version of your T2 scan? It’s the same voxels, but with a rotation + translation in the header (see attached screenshots).
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2B...
*From: *Wei Shao wshao@research.baycrest.org *Date: *Tuesday, March 9, 2021 at 13:06 *To: *"Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution *Done.
On Tue, Mar 9, 2021 at 12:29 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Thanks, Wei. I’ll need the T2 scan, too, to reproduce the error…
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2B... http://secure-web.cisco.com/1Fx61iJxDyYVe2fnrRp0RtspkT-zKv5Bc7Y63jGXjLR_cqDvugirJ9o75TTwbk0aMVUGaSGXbXJZCuvv5jtoQCpVekv21Mye77SCsudpm0kCkk2QqBLhCZXVOaJBYBH5i36w0Bz6FMNSxfnwEdUk_jzo837ZwG6Q3Tpp_n1HKxN4Nb1qH6U5iaHgurQgMkAFKXRhJuTWYw9hW_elL-f0exWctfFVP1jMZfCAJZGy1UhHmkB2UAqa03cWMBN8DOK0dZPJNNDgtyzNFasisUwkf8w/http%3A%2F%2Fwww.jeiglesias.com
*From: *Wei Shao wshao@research.baycrest.org *Date: *Tuesday, March 9, 2021 at 10:50 *To: *"Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution *Yes, that's right.
On Tue, Mar 9, 2021 at 8:53 AM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Thanks, Wei.
Just to confirm: It is BAY11958.rar, isn’t it?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2B... http://secure-web.cisco.com/1zPyhHavtDe-BOf3ONc0w_hrwPGxdAWLBdw_UFdk6DvDm2IJLqdf6kAJd87D0pgy88d7Vv7Z3GGluz0igKvFhvO9rX1Y9rPEGyD1hYK6oVLO9zmrwNvatgiYl9qv0CtRWHtD425hX_AM0WVSKem8pBYaC-UbQ9kLB5kvKTJK51sYIq7iUHajlOx44-pFLRXG1YQ37RLoiBz5mZQ1hUgmMR8Tb9eZoAKwDLRl9EvOrqxFqNHMQXuGmR2dexUC3W3WDKCqjBKsWvp47gh6tKK_fQQ/http%3A%2F%2Fwww.jeiglesias.com
*From: *Wei Shao wshao@research.baycrest.org *Date: *Tuesday, March 9, 2021 at 01:16 *To: *"Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution *Hi, Dr. Iglesias
These are the files I uploaded before.
Thanks for your suggestion, I have uploaded the subject as well.
Best,
Wei
On Mon, Mar 8, 2021 at 9:26 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
(sorry, I hit “send” by accident)
If these are indeed your files: the hippocampal segmentations seem to be there for both hemis, am I missing something?
If these are not your files: please upload the whole subject (not only the mri directory) as a single zip file.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2B... http://secure-web.cisco.com/1dN2TtIR95Q_e7HDyPOAO1rPpEjgUKkGjmDO6ykSOveSEnTwYLOcrxeNRDe9oNCVSFrPdbaPhHNv6TQU7rRtw8gysMFellbtKgKeRFlFs0y2XINE6oPjLnqJJiZguH45eNUhsxCn-PWfJiS8eil_61CSmsYLBlZcSPAD7MopaVWaJG79WQkECgShpm7CGWdljOursiXSinv3MYE7pBSsVA9jxfO9Tw4vsYMY9HHVKR9MiBj8OWkMPahwdo03P3tPWhQAvko4AURxoy6su8tMwFQ/http%3A%2F%2Fwww.jeiglesias.com
*From: *Wei Shao wshao@research.baycrest.org *Date: *Monday, March 8, 2021 at 20:10 *To: *"Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution *Hi, Dr.Iglesias
I have uploaded most of the files from mri but some uploading files are failed due to the permission(I guess)
put: Access failed: 553 Could not create file. (rawavg.mgz)
lftp surfer.nmr.mgh.harvard.edu:/transfer/incoming> put orig_nu_defaced.mgz put: Access failed: 553 Could not create file. (orig_nu_defaced.mgz)
Also, the whole directory
mirror: Access failed: 550 Failed to change directory. (/transfer/incoming/BAY11958) mirror: Access failed: 550 Failed to change directory. (/transfer/incoming/transfer)
If you need any other files, please let me know.
Best,
Wei
On Mon, Mar 8, 2021 at 9:38 AM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Happy to hear it’s only one subject!
You can use the Research Computing Secure File service if you want.
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2B... http://secure-web.cisco.com/1CafarPRKDaufU2h-Ym1LPWx_e9ZvgoO6OTY2wq9_75MBpaMlHoFGT4MWaAA6g-XNtvxHTd_Yb3PVt7Dkttj86F8x75x3gsznEwGAnm_TjehftOkD0-z5VGIdiGroQyKIvCO-EElfSW0QywQaAtVK1xEZDjQMYm4kyKfi1w8s-s7yuhQsxWXP3ZyR151--J3_fg2SSyJ677cyecnpJJdvtEK-R8QYKETaaR9kNM_QNUGMNCCxo0GPC4QJVXMJrERYsuzYEprDDrPfo7IVZB4ACg/http%3A%2F%2Fwww.jeiglesias.com
*From: *Wei Shao wshao@research.baycrest.org *Date: *Sunday, March 7, 2021 at 16:35 *To: *"Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution *Hi, Dr.Iglesias
Sorry for the late reply.
1 This is a problem that existed in a single subject
2 The data is on the Server I'm afraid that I might need to ask administrators to install FTP module before I can upload it. FileDrop has removed and I'm not sure I can use Research Computing Secure File service https://secure-web.cisco.com/1eBAVZsWWR_HCPD2RJhlVuKHa_7f7u6W3sPkSdbuB3GdKuvOQwBomw6B2zQfr5aUpObQvYLLJjPkkmOMo9FcO9xWDOaGOlc3inXRaQcp-G-0WZyjfTykD-E0VSGfkA9n6G0h-9L_2KSsauVyLOtpeCRI0W3hDqips3WE4h6AuZQxjL4eyaW30h7tRwFmpYWwdW0qhVbw8Np64NaNebJJwwm5bs8zda0wVrjdS6G4cxO2dMlwawLALjO1NGsvxbvQjBZcOXG44t2oP3Ch4QHjNGw/https%3A%2F%2Ftransfer.partners.org%2F nor not. Do you have a more convenient method for me to upload the file? Thanks
Best,
Wei
On Tue, Mar 2, 2021 at 12:32 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Thanks, Wei, they look fine…
Two more questions:
Is this a problem with a single subject or a more general thing?
Would you mind uploading the whole subject directory to our FTP so I
can take a look? https://secure-web.cisco.com/122B5Ozj3vqhOd7S4iEyZWCdDjb91Ert2uOyO9hFEwx0hvr... https://secure-web.cisco.com/1l9A6PhiKog1O8l0piwPOJ6bVu4No6QoNXKbm9BKNoWk2KdFPaf8f-I3mUdn7HfNRTADNdd2Y-VRnfZrH-ahRHCFCBqa6a5fzfXikSvh086ygS4l3hU_qnHbzTJiPY1zVtnY5IuldpQqUpfAndcrN29jLAt_94jVdOofm7w8UqVQo9j9YEIkxz_qA4E1gqGScYy-o_pW0s-pzYPM7fdjFHsw_HUd2xpFEdWzXrqPu3eSh6eeTV76uNWWiixAfJBNWiOB_wTD7a-OWPF5ZeuQW-w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFtpFileExchange
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2B... http://secure-web.cisco.com/1qOJOLNYddAE1LFZgcFcqi_Px5RF7gEt4AaZLTL5qeaUwNeQZSw3dmUYKjnBH65bNwvuibu7XG--6zN2D1SktPUgA75Oc5S3vThC6S_ug4ZU4nlyB8q0O3n_CEohYPVkaNSTso0QjWD71iTMTfUJGjuJ_9jnPPzb7yWhyb8ikgv_sl4OpC3ERdjueXzUIJQIE9QTcTfuHgU8wonnBlusTNSP_b_yg9gBlgY1cov38NkNjr_mWVPM52Y67SUpJfvNP0Ft46aCm6gq477JupFerDA/http%3A%2F%2Fwww.jeiglesias.com
*From: *Wei Shao wshao@research.baycrest.org *Date: *Tuesday, March 2, 2021 at 12:29 *To: *"Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution *Hi, Iglesias
It's ok.
Here is the aseg.mgz, I'm not sure whether this is good enough? but I have attached the norm.mgz and aseg.mgz in case you want to check.
Best,
Wei
On Tue, Mar 2, 2021 at 11:43 AM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Sorry for the autocorrect! Wei -> way
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2B... http://secure-web.cisco.com/185AprJjk1YWZOkgwrwFKQd7HgW56kk_VXXxriE36u523IXgZwi0ebBHzaRaefnFiXMwzhXgiBMTQaFP3D3txyDMUXd-F3ZyReHsbhEX0Rj94v9ywQ7HT935o_KEp3Trw9We3w7oKWDRPJxsHHCAkafFlgYN3jjOTtk7yTdf9MY1sqpOsE65NhIIGpKIFZ6ScZyjXCzY5mRwvQp5Q28OoOWJ0DJC8oJxPziQCL7tYhqnTY48YUCHuvI_AVI8o7T8WPxxBYve4JYgjdd8aCkXDBg/http%3A%2F%2Fwww.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: *Monday, March 1, 2021 at 23:40 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution *Hi, Dr. Iglesias Gonzalez
Here is the full log, Thanks
Best,
Wei
On Mon, Mar 1, 2021 at 10:33 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear Wei,
Can you please provide us with the full log?
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/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2B... http://secure-web.cisco.com/1QG7uGIHTOdZ2Mb_tpU68iZ_owRYsTQl1DBCO6QrSAb64Kb0Rzx4ZOx3LNeUg8cYWEvLm-ybTeV1JGTHuVgY1mPHQkB2CmTV1abh94ZqQMIdEuu9BWHGad2nW93ap3bPSQo7vfA2A8K_RNQcgq4iyn6EPQbMinxBF5sIhnLQ8afvzuSH1H7FKJPfFaASueXmm0wAWzLcQfenpnINPHN0pxmolEUVEIxDvF6S9Sy1lCrwLo2vFrA_dVs0tjaG_TwJXCb4SCij-8ijuqTNnJ26T-A/http%3A%2F%2Fwww.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: *Monday, March 1, 2021 at 21:14 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Hippocampal subfield segmentation
External Email - Use Caution *Hi, Freesurfer expert
I tried Hippocampal subfield segmentation with an additional T2 scan by using FS7.1.0
Here is the log error massage
Attempted to access cropping(1); index out of bounds because numel(cropping)=0.
Error in applyCropping (line 7)
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 950)
MATLAB:badsubscript @#@FSTIME 2021:03:01:20:38:39 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 e 243.67 S 3.47 U 220.01 P 91% M 1248336 F 144 R 909119 W 0 c 49601 w 14948 I 320352 O 429920 L 30.66 34.91 35.10 @#@FSLOADPOST 2021:03:01:20:42:43 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 47.20 43.27 38.55 Linux gra813 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Mon Mar 1 20:42:43 EST 2021
For more details, see the log file /home/weishao//BAY11958/scripts/hippocampal-subfields-T2.T2.log
Could you tell me how to fix this? Thanks.
Best,
Wei
Freesurfer mailing list 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/1KRElfcByalckdH0eSE8KoyDaKBoB93IA7qkOJJEYYynjO3... https://secure-web.cisco.com/1yoXS6dKZ-NgQmNn6ZWsu7E6Fy28mmAvwujVOWjd0TXC-2rnYtbfOToNdj8FNRMl9_r5G8pvA0y52cLEZFh6ArDsWdkuOwbOa_KluGStvj2OQyVepzLH4HE5ODIpzKRsK15XP970jorSINqsZRyBgnFcxFZJRes9cFrFSURI2jqckcNTD2AWH86HiraJqydQcHdqq2GxQ-BMsVtdOi98xqbXk3kJAxAf1hR-bNclwgewkP4DdSlUYTpBkzn5HP-hCNXbNCr3uIvKMC0MLJz68nQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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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/1fbEBF3dojblctBXJdzmGvBItNipo3eitWhFwcRkSgDNJE8M... http://secure-web.cisco.com/1s2luIsQugmABYuuhe95L3m3voeMDT0jlubdn0AdJjs4LTFSTyyDmByaHR3wUXHWhmxLOwIiuVLeTA0TPYFsN_fehe6ahqxMNKB1y8I-dkMNSeHm9OqjJ9ZJIGT7R8vkzdUx2ARq4gFIKnp2D_d0DeTqZdDNDcaN-4wcFBOkwxh7Llw9c9RlhdAM6rHHXjakOFHnUDnp-e_jMy0_-6Fu4G99AyZ-B07RmNlxvDqz9awOHiELoJJdlYI3ARmWGf93a-abJOP3Et9od4yqLwtRIoQ/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.
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/1fbEBF3dojblctBXJdzmGvBItNipo3eitWhFwcRkSgDNJE8M... http://secure-web.cisco.com/1Vv4wBtT7JnsV1obCAtwOakbaJYG9UnKR7Fumz2P0vs4K1BAEay3mmHNbpGwhVmFu24HX_Mu8EM8D9-f30KdHNHmiNXGEgHkT965qhllTx3U1gbsnmHai_myjLImIcOJW5Vc4CmXNHvgdIbDJFZq4lRYbbWOQR_Z-JM-mJKcjYgLxoi80bPvH3p1i7jJTcFQKB0eV9s6fBnG7sNLP_itG4QHRptuGMq73s27KBy1x3p6s8S1V6qp3XNHWWLb_5KKuwi1wiE6QeA_mwyyjpqdGUA/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.
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/1fbEBF3dojblctBXJdzmGvBItNipo3eitWhFwcRkSgDNJE8M... http://secure-web.cisco.com/1u-8lX17UNPf6f0qqn-RcMei0JiQ5dR3vpa3qQmopZX6BA2FTNczt1jRxB4bhNsOHXW--8yozcYGZob3L8v5v710aBrFNZTZTayZNEcoKYJCGQh6EyVdtPm6EyTp9IkAhlED5ijWE15KAGXFlVav0VMRJ3AHVisrbxx4P4cCTYHK3tP2ysG48uoaF6pI16bL5sE1dfoXO6H2tJM2GoTRoXD8wj3R1o92OfZK0sm8A1ehxpkuvpaTP7rlv7r9GDnD-1v6ghiYUn4HLMW1NaMML_g/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.
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/1fbEBF3dojblctBXJdzmGvBItNipo3eitWhFwcRkSgDNJE8M... . 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.
