Dear Wei,

These are resampling artifacts when visualizing a highly anisotropic volume on top of another volume (eg the isotropic T1), which forces an ugly resampling to occur. You can avoid this by opening the T2 first, and then the T1 on top. You can further ameliorate these artifacts by choosing linear or cubic resampling when opening volumes.

Cheers,

/Eugenio

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: Thursday, March 11, 2021 at 13:23
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Fwd: Hippocampal subfield segmentation

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---------- 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

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)

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com

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)

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.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

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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)

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.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

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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)

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.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

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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)

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.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 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:

1. Is this a problem with a single subject or a more general thing?

2. Would you mind uploading the whole subject directory to our FTP so I can take a look?  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Cheers,

/Eugenio

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.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

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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)

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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: 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://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: 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

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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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/complianceline . 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.

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