Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)

[fsbuild]

External Email - Use Caution

In your terminal window after you’ve sourced the freesurfer setup script you 
should be able to do,$ which freeview
… and it will show something like …
/usr/local/freesurfer/bin/freeview
So using whatever that absolute path is to freeview on your system, then do,
$ ldd  /usr/local/freesurfer/bin/freeview | grep not
If you see output that says a library was not found, then something is not 
right with your system - which could explain the segfault.  In that case I 
would try to find a way to download and install the freesurfer 7.2.0 Debian 
package installer as that should install any missing 
libraries.https://secure-web.cisco.com/17qbBdi-wXIfcvgJHoFSyqwZNNfccEzYQiqaLM3KKP1GfRbI3U94aISVOv9a0YGhQd-FCtmmbw7EmGlkXloHQKHGR5kQ0Ohxp0JGux2qcz8j5Rt8B1ctRfTvIV0UnaEl1nURjUsgCYtjC_sdG7KQX4ngvB3LSoCGEbOfNmi6oSxEaLWw_txh_79zUoOTNlVLgJDc-Aiw0gVqTJZNFknHkH8hauq6pkHSeBkQOXmK_JglhjC6WkKJ7lxYocce_WbdghbeaKkfQAYCYs_29qmOAYZN6dGIMzsWXk3nEcX4_2o-8BIcJbPHPV8yjzL-ug7MmedUYalixU7ncC7ps_gf7gA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz
If no libraries are reported as missing for freeview, then if you have not 
already tried the variations on setting DISPLAY listed at the end of this page, 
then I would do so, 
https://secure-web.cisco.com/1ZTeXQ90uTtWNjlyitGyKt3hbJVwUsSL_sYysu7DQgUWeVYEJ3df0g2306v_BSgfcZcf-O-h84P8FI1bM8w6NvXdRDfn8OmNn3Bd2V_G3xAgU6xj4cUCTfEb713wXDGFlgtPBlmY8DpBUgV5sW4LgTOtwmG4nrBFDvr7sTDlSADHJxgc65FfWf__QvgO9AXBeGjue8kk34zd9MWvvU4rcxgnyVLxMPmKN4iPYD0FXifn62v010k6baCbhiM-My8JXv-HZT-AtXOYDaZqqe6lpOJxP5BDg8rXv8rApcm1Xiy-kKg73gkr8CeS_jMpXPsNPuk9XGaMpHUUQWsSXV1Cbnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu
   You may have to use your IP address and append :0 or :1 to it.
If that does not work, then send back your default setting for DISPLAY and I 
will check with other people who use the WSL setup.
- R.

On Nov 17, 2021, at 21:02, 许霄  
wrote:External Email - Use 
CautionI downloaded a license 
file, and copied the content in it to a new file created in $HOME path, 
named the new file 'license.txt'. After that,  reset the environment 
variables:$ echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> 
$HOME/.bashrc$ echo "export DISPLAY=:0" >> $HOME/.bashrc$ echo 
"export FREESURFER_HOME=/usr/local/freesurfer/7-dev" >> 
$HOME/.bashrc$ echo "export FS_LICENSE=$HOME/license.txt" >> 
$HOME/.bashrc$ echo "source 
/usr/local/freesurfer/7-dev/SetUpFreeSurfer.sh" >> 
$HOME/.bashrcMeanwhile, to test if Xming was running, I executed xeyes, and it 
worked. But the same error "Segmentation fault (core dumped)" still appeared. I 
found that there was no .xdg file under $HOME path, mentioned in the 
command"export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc". Please see 
the details in the attachment. What should I do to fix 
it?Best Xiao-原始邮件-发件人:fsbuild 
发送时间:2021-11-18 03:05:29 
(星期四)收件人: freesurfer@nmr.mgh.harvard.edu抄送: xux...@xii.ac.cn主题: Re:
 [Freesurfer] freeview error after installation: Segmentation fault(core 
dumped) / free( ): invalid pointer, Aborted(core 
dumped)External Email - Use 
CautionHello, Xuxiao,You need 
to go to this URL, MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1-AZrSjO8Cl_Hc1uoojvBIGTFics6sBFWG99iZ-P1u3LukFGKniPlUm-E-VGjcRE_b-5E-iOvjqEZNnuGOgCw2Pkg1-eC-UxfUhNvM4PC4oeD-yGP31_5V7cBwdiywW09KhcDihFjOvJSLlMoqKyKIkSMftWf7jNXb3CzOUgWTiSKzJ6V7cP5ooLjf7jC6_Z2fma3-7ssLtdEbEYZL3t9_hHSX43mODgn8iO_TikKgwbVAJLuq6_dxHjhTZd2oIhm1adZDW1MzIDHvFsP_f9Gx49oAoTHPuuFB7gACzq83ISkU93lG2zQlUZjeTqIoCu3Y65c2oY5Pd95FlbeLROCOg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html,
 fill out the form and agree to the terms of the freesurfer license.  Then 
you will be able to download a license file.- R.On Nov 17, 2021, at 06:10, 许霄 
 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers, According to your reply, I found that xeyes worked, but 
there was no license file. I thought the license file would be 
created automatically after installation of freesurfer, or by the command 
"echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc". Do I need 
to create a license file manually?-原始邮件-发件人:fsbuild 
发送时间:2021-11-17 10:16:00 
(星期三)收件人: freesurfer@nmr.mgh.harvard.edu抄送: xux...@xii.ac.cn主题: Re:
 [Freesurfer] freeview error after installation: Segmentation fault(core 
dumped) / free( ): invalid pointer, Aborted(core 
dumped)External Email - Use 
CautionHello Xuxiao, In a 
terminal window in Ubuntu running under WSL, please try just running a simple X 
windows program like xeyes to test that your X-server is running on 
Windows, $ xeyes(see attachment for what it should look like)Keep an eye 
out for a flashing X server icon at the bottom of you

Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

[Fischl, Bruce]

Hi Noam

How much ram do you have in the machine? Is anything else big running? You can 
also examine that defect and see what is going on. 9000 vertices is pretty big 
so something significant like a chunk of skull might be fixable

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam
Sent: Thursday, November 18, 2021 9:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

Thanks Doug!
Unfortunately, removing the parallel flag didn’t help:

“ …
After retessellation of defect 43 (v0=79551), euler #=-51 
(145804,431777,285922) : difference with theory (-68) = -17
CORRECTING DEFECT 44 (vertices=9236, convex hull=4698, v0=79649)
Command terminated by signal 11
@#@FSTIME  2021:11:17:14:54:07 mris_fix_topology N 14 e 12788.52 S 1.14 U 
12786.35 P 99% M 1761016 F 0 R 581366 W 0 c 79248 w 3 I 0 O 3960 L 1.01 1.00 
1.00
@#@FSLOADPOST 2021:11:17:18:27:16 mris_fix_topology N 14 1.00 1.00 1.00
“

Any ideas?
Thanks again,
Noam

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Douglas N. Greve
Sent: Wednesday, November 17, 2021 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

I'm not sure what is happening. Does it work without the parallel flag?
btw, you are not using 7.2
here's your build: build-stamp.txt: 
freesurfer-linux-ubuntu18_x86_64-dev-20210824-e101185
On 11/16/2021 4:26 PM, Peled, Noam wrote:

Dear Freesurfer group,

I was running recon-all (Freesurfer 7.2 on Ubuntu) and received the following 
error:



“

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig 
orig.nofix -out orig.premesh -ga -seed 1234 UC07 rh



Waiting for PID 6337 of (6337 6340) to complete...

Waiting for PID 6340 of (6337 6340) to complete...

/home/basuia/Documents/mmvt_root/freesurfer/bin/reconbatchjobs: line 77:  6340 
Segmentation fault  (core dumped) exec $JOB >> $LOG 2>&1

PIDs (6337 6340) completed and logs appended.

“



Please find the log file attached.

Any idea what is the problem?



Thanks,

Noam


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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

[Peled, Noam]

Thanks Doug!
Unfortunately, removing the parallel flag didn’t help:

“ …
After retessellation of defect 43 (v0=79551), euler #=-51 
(145804,431777,285922) : difference with theory (-68) = -17
CORRECTING DEFECT 44 (vertices=9236, convex hull=4698, v0=79649)
Command terminated by signal 11
@#@FSTIME  2021:11:17:14:54:07 mris_fix_topology N 14 e 12788.52 S 1.14 U 
12786.35 P 99% M 1761016 F 0 R 581366 W 0 c 79248 w 3 I 0 O 3960 L 1.01 1.00 
1.00
@#@FSLOADPOST 2021:11:17:18:27:16 mris_fix_topology N 14 1.00 1.00 1.00
“

Any ideas?
Thanks again,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Wednesday, November 17, 2021 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

I'm not sure what is happening. Does it work without the parallel flag?
btw, you are not using 7.2
here's your build: build-stamp.txt: 
freesurfer-linux-ubuntu18_x86_64-dev-20210824-e101185

On 11/16/2021 4:26 PM, Peled, Noam wrote:

Dear Freesurfer group,

I was running recon-all (Freesurfer 7.2 on Ubuntu) and received the following 
error:



“

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig 
orig.nofix -out orig.premesh -ga -seed 1234 UC07 rh



Waiting for PID 6337 of (6337 6340) to complete...

Waiting for PID 6340 of (6337 6340) to complete...

/home/basuia/Documents/mmvt_root/freesurfer/bin/reconbatchjobs: line 77:  6340 
Segmentation fault  (core dumped) exec $JOB >> $LOG 2>&1

PIDs (6337 6340) completed and logs appended.

“



Please find the log file attached.

Any idea what is the problem?



Thanks,

Noam



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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://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.
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. 

Re: [Freesurfer] Hippocampal Subfield segmentation problem - Matlab exits due to fatal error

[Georgia Kapizioni]

External Email - Use Caution

Actually the same error occurs with thalamus segmentation also. 
I made the change you suggested on resolution at the segmentHA_T1.sh (yet I was 
not allowed to make the change on the initial file so I created a new one) and 
now when I run the command it says: "permission denied”. I tried with sudo and 
it says “command not found”. 

Any ideas on that?
Thank you once again for your immediate response!

Georgia


> On 18 Nov 2021, at 10:55 PM, Georgia Kapizioni  
> wrote:
> 
> Thank you so much for your reply Eugenio.
> 
> I have 16 GB of RAM. Do you think this would be a problem?
> 
> Thanks again,
> Georgia
> 
> 
>> On 18 Nov 2021, at 10:04 PM, Georgia Kapizioni > > wrote:
>> 
>> Dear Freesurfer experts, 
>> 
>> I am trying to run hippocampal subfields segmentation, using the command: 
>> segmentHA_T1.sh subject
>> The analysis is running for approximately 20 mins and then the following 
>> error appears:
>> 
>> f this problem is reproducible, please submit a Service Request via:
>> 
>> http://secure-web.cisco.com/1bAOeeu-yT9Ghsf3DgdHjQExvDxgifx7t9eLoK-E797kgPyuk5FQHH64FDyPTOI9anMEuPHYLGqcKwvw5pevb7x89Fvhew6AZuZOi3AGkq1DT0qgzzIXlTNfTS_sQOTos2SMFSwo2ept162uhYGghknEloTanE0GpM9yRwLMcbiN3nG4LYjFlygvZts_rtH7LUhka6JhJOc9cGBy42DM5eT3x8RNgJUvWAMT6VO1jF9k5jN6I_bz7kJqopSLOOUXVlI-c37UfoKymMwXQSFuf0scRXho8Dvf7FyAE5PxHH8KtKhyolPV0MA3V6DpUcs6A/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
>>  
>> 
>> 
>> A technical support engineer might contact you with further information.
>> 
>> Thank you for your help.** This crash report has been saved to disk as 
>> /Users/theodore/matlab_crash_dump.4118-1 **
>> 
>> MATLAB is exiting because of fatal error
>> /Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
>>  line 33:  4118 Killed: 9   
>> /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
>>  6529 /Users/xxx/Downloads/xxx/qcache 0. 
>> /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz 
>> /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz 
>> /Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt
>>  0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr 
>> /Applications/freesurfer/7.1.1/bin/' 0
>> Darwin MacBook-Pro-Theodore.local 20.3.0 Darwin Kernel Version 20.3.0: Thu 
>> Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64
>> 
>> T1 hippocampal subfields exited with ERRORS at Πεμ 18 Νοε 2021 15:34:58 EET
>> 
>> 
>> Attached please also find the script output. I am using the 7.   1. 
>> version of FS. 
>> 
>> 
>> Could you please help me resolve this issue? 
>> Thank you in advance,
>> Georgia
>> 
>> 
>> 
> 

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Re: [Freesurfer] V5 / v7

[fsbuild]

External Email - Use Caution

Hello Ludovica,
When binaries (libraries and commands) are built with different (newer) 
compilers and/or run on different (newer) versions of an operating system, then 
the numerical results aren’t guaranteed to be the same between between 
releases.  See the IMPORTANT NOTE at the bottom of the downloads 
page, https://secure-web.cisco.com/1Of-G3pv8_jYIju10j21uSajW2HRrYUJxk99PrFVwRfoYSlAsUb3S6Uk4qP2wf23EVH-cI_skGDSdBReSdm8NK_iXQJugbArtbYFTwIjvNLoRoNqPK4C7gky4rOzN5IXzwJUi-e8rGnJCk8DJWWWXX_xROG7j4mAVCQ0kjZYUTLhNTTmKKRXiCvVsgSo_xHkRFxgNBKECkbC1N2CozUybZSD85e6RnE0n3fbqoategMwYGJHrN-R-jRWnGi_hsVOz8DmHHo12w64CiArsRUZJFlJrjVLJXNYsaxDtouc58qCwEMf9etwHuozXYOHvB-XwS9sVxbqpQ_Js1b1Yh1pu7A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
Apart from being built with newer compilers and operating systems, how specific 
commands perform computations may also have changed in version 7 compared to 
version 5.  See the release notes for versions 6 and 7 on this 
page, https://secure-web.cisco.com/1NuFoGxg65bB9oU3RVYIhCjgc245S9FNl9WzWK2BvnUmLv-wQGfVg7INR6ljTAexgHWGMyFaICjBkBVWTxparjkl_jyh94fU2rGz3mka485H_VMIW-4RJdtIA4WmHogUywmvcFf93PmpABMM42kN8zTGJS8wL-Zt90wffI9zhn-bKiAmv_FK0vPUsWYtLC_oPEpp2B_m5po7Co_tF0qPiJ2R-IKh9NVk4XrFpYANGh7loehifea2eAcWXxbbpxNf_hTHVzplBpf6NkAqpXx7zuzS_YXVhqqIwHaSh_Ba6x59Eqg_VvOXv3vGud5O_bvlmzJQvCisa23zZmB-AeNOcmg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
If you are interested in the development history of an individual command, then 
you could look at the source on GitHub and read the log of changes.  For 
example, to look at the development history for mri_glmfit, you could route to 
https://secure-web.cisco.com/1qq01hy_US_gpsCh6hj0XMtzJwWQV_PcnJdrYJJllMgKQgoV8tiVFw4ETby_rLab8RqfwuNUDNtsbt2GAQCpHT_pAmRTupiFqOYDv6-PgkffHiQbVf0mGbqG55HvdgbZAP1XAO-ezo8kUglxAognsFK-RXZ_2rmcMDCzIpPVYaRZfR1K14LJN0M0fzBd8qlJ5CnIhrbIP3S2cgssKc0RJQbACS87YRs2VXgrE0op_FbBuX2b--Yc-p6bgr0bgS4Vb1F5h4P6JW_Owx5U-t1tNO4u_7C2_q8t_JJzSut96akih5fxGfy5-dZtHqZAa6-DIzU5U2Sopzoul2mdkJ6oS0w/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Ftree%2Fdev%2Fmri_glmfit
  and then click on the text for “History” near the top of the page on the 
left hand side.
- R.
On Nov 18, 2021, at 14:03, Brusaferri, Ludovica 
 wrote:Hi!I am using a pipeline that was 
implemented and validated using fs 5.3 , which does the following:* compute 
transformation matrix for linear registration of SUV with T1-2mm, with spm* use 
tkergister to transform the matrix into .mat, and then invert the matrix* use 
flirt to move T1 images into PET spaceThe last step gives me different results 
if I enable FS vs 7, and the registration seems to be off. Do you know why this 
would be the case?Thank 
you!Ludovica___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Hippocampal Subfield segmentation problem - Matlab exits due to fatal error

[Georgia Kapizioni]

External Email - Use Caution

Thank you so much for your reply Eugenio.

I have 16 GB of RAM. Do you think this would be a problem?

Thanks again,
Georgia


> On 18 Nov 2021, at 10:04 PM, Georgia Kapizioni  
> wrote:
> 
> Dear Freesurfer experts, 
> 
> I am trying to run hippocampal subfields segmentation, using the command: 
> segmentHA_T1.sh subject
> The analysis is running for approximately 20 mins and then the following 
> error appears:
> 
> f this problem is reproducible, please submit a Service Request via:
> 
> http://secure-web.cisco.com/11Mc3CMrLGgkPD-QRis2_uj_aniCfHMJdirWPDO6Lv4rlGzfTrDQ_DRUfamZnfjWsXSrUNMheFJUGqpeoDn3rLhFQ7OFNuwLuc4dmn-EP6fpz8iItS8-7G9F5VNi04adeNc_ktzSYv-5UYFOOzJyTw_gdAdy7JqzbMD_2RkmsMThSOkvX0kLu1186qGOrFR-Q6g5tam8tRbpDLS2RV6iO9Zone-6AK3JQ6aIQmsy8Ti88BukKMOnLhiZLvz1rXfgrU0BRmgBxXXnVSEFG45tfRYCVm38_iIYliwM026X5uSU8LOcyFB5Kc4K7e4ujivf98WgmoZO7D9Uf5bJtehPs-Q/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
>  
> 
> 
> A technical support engineer might contact you with further information.
> 
> Thank you for your help.** This crash report has been saved to disk as 
> /Users/theodore/matlab_crash_dump.4118-1 **
> 
> MATLAB is exiting because of fatal error
> /Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
>  line 33:  4118 Killed: 9   
> /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
>  6529 /Users/xxx/Downloads/xxx/qcache 0. 
> /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz 
> /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz 
> /Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt
>  0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr 
> /Applications/freesurfer/7.1.1/bin/' 0
> Darwin MacBook-Pro-Theodore.local 20.3.0 Darwin Kernel Version 20.3.0: Thu 
> Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64
> 
> T1 hippocampal subfields exited with ERRORS at Πεμ 18 Νοε 2021 15:34:58 EET
> 
> 
> Attached please also find the script output. I am using the 7.1. 
> version of FS. 
> 
> 
> Could you please help me resolve this issue? 
> Thank you in advance,
> Georgia
> 
> 
> 

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Re: [Freesurfer] Hippocampal Subfield segmentation problem - Matlab exits due to fatal error

[Iglesias Gonzalez, Juan E.]

Hi Georgia,
How much RAM memory does your computer have? Is it possible that you ran out of 
it?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



On 18 Nov 2021, at 15:04, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:


External Email - Use Caution

Dear Freesurfer experts,

I am trying to run hippocampal subfields segmentation, using the command: 
segmentHA_T1.sh subject
The analysis is running for approximately 20 mins and then the following error 
appears:

f this problem is reproducible, please submit a Service Request via: 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.mathworks.com/support/contact_us/
 A technical support engineer might contact you with further information. Thank 
you for your help.** This crash report has been saved to disk as 
/Users/theodore/matlab_crash_dump.4118-1 ** MATLAB is exiting because of fatal 
error 
/Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 33: 4118 Killed: 9 
/Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 6529 /Users/xxx/Downloads/xxx/qcache 0. 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 
0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr 
/Applications/freesurfer/7.1.1/bin/' 0 Darwin MacBook-Pro-Theodore.local 20.3.0 
Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; 
root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with 
ERRORS at Πεμ 18 Νοε 2021 15:34:58 EET


Attached please also find the script output. I am using the 7. 1. version of FS.


Could you please help me resolve this issue?
Thank you in advance,
Georgia




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[Freesurfer] V5 / v7

[Brusaferri, Ludovica]

Hi!

I am using a pipeline that was implemented and validated using fs 5.3 , which 
does the following:

* compute transformation matrix for linear registration of SUV with T1-2mm, 
with spm
* use tkergister to transform the matrix into .mat, and then invert the matrix
* use flirt to move T1 images into PET space


The last step gives me different results if I enable FS vs 7, and the 
registration seems to be off. Do you know why this would be the case?

Thank you!
Ludovica

smime.p7s
Description: S/MIME cryptographic signature
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[Freesurfer] Re: longitudinal analysis – Is correcting the Base enough?

[Mora, Jocelyn S.]

Hi Eszter,

Yes, you can use the base for quality checking and editing. In some cases you 
may need to check the cross-sectional runs for a subject --but it is especially 
important that the base is accurate for the longitudinal runs to be accurate as 
well. After editing the base, you shouldn't need to make edits to the long runs 
(or at least very minimal edits should be needed).

Best,
Jocelyn

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eszter Boros 

Sent: Thursday, November 18, 2021 12:13 PM
To: Freesurfer support list 
Subject: [Freesurfer] longitudinal analysis – Is correcting the Base enough?


External Email - Use Caution

Dear FreeSurfer Team,

I am working with a longitudinal design (before and after treatment), and based 
on the website's recommendation (MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits)
editing the Base could be enough for this.

If I understand this right, I should generate the Base image (without editing 
the two Cross images) and then edit the Base only.
After that, I could create the two longitudinal runs (Long) without editing 
them as well.

Did I get this right?
This could save a huge amount of time since I should edit one image (Base) 
instead of two (Cross images).
I am using Freesurefer 7.1.1.

Thank you for your answer! I greatly appreciate it.

All the best,
Eszter Boros
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] longitudinal analysis – Is correcting the Base enough?

[Eszter Boros]

External Email - Use Caution

Dear FreeSurfer Team,

I am working with a longitudinal design (before and after treatment), and
based on the website's recommendation (
https://secure-web.cisco.com/1zrVKA2yLWZKJu8t_xqtLsDY49D7WzDkL9DDKJIkf-aD-ta0MoxVsjvpA3mU7AatuLy2HhTTrGBfLjCwCV1vfWzdjfnQxQ9puAXzqSOBHSdsbvgzbKlyMiAWuakKR9YRIz_3ll1jldx-lPT1TTydguj6Y2r5d3SBZ02eny7yjuawPxEqdxjJnE3JWxUyIVJtFBaqeuZh51foNHb1fgnqoz9kmNTobjj8B0Y4BHbENMXGT9XJ0PShQ1ZH0HVhzgOS91R_5mHWy2iWc41XH7MeGsY6M-sS7UMUhZrzUWwEsHzzs_jfxFMOUrKAp4aAhCYI4CPjtR1iZWMlVqsU0uQXWuQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalEdits)
editing the Base could be enough for this.

If I understand this right, I should generate the Base image (without
editing the two Cross images) and then edit the Base only.
After that, I could create the two longitudinal runs (Long) without editing
them as well.

Did I get this right?
This could save a huge amount of time since I should edit one image (Base)
instead of two (Cross images).
I am using Freesurefer 7.1.1.

Thank you for your answer! I greatly appreciate it.

All the best,
Eszter Boros
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Re: [Freesurfer] Help

[Fischl, Bruce]

Hi Nilab

Can you send us an example? Usually you can fix this using expert options to 
constrain the range of intensities that white matter is allowed to take

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nilab Nasrullah
Sent: Thursday, November 18, 2021 8:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: gr...@nmr.mgh.harvard.edu
Subject: [Freesurfer] Help


External Email - Use Caution
Hi,

I am editing about 120 subjects for a research project. In some 
reconstructions, the grey matter boundary is not recognised, thus Freesurfer 
classifies it as white matter. I have tried to remove additional pial surface 
in the area and it gets a bit better. I have also tried to erase the wm that is 
classified as gm but the results don't change. Using control points is useless 
since the white matter is classified correct. Is there any way I can edit the 
subject to get better boundaries for the grey matter?

Thank you for your help in advance.

//Nilab Nasrullah





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personuppgifter.



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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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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] Help

[Nilab Nasrullah]

External Email - Use Caution

Hi,

I am editing about 120 subjects for a research project. In some 
reconstructions, the grey matter boundary is not recognised, thus Freesurfer 
classifies it as white matter. I have tried to remove additional pial surface 
in the area and it gets a bit better. I have also tried to erase the wm that is 
classified as gm but the results don't change. Using control points is useless 
since the white matter is classified correct. Is there any way I can edit the 
subject to get better boundaries for the grey matter?

Thank you for your help in advance.

//Nilab Nasrullah



När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI 
kommer att behandla dina personuppgifter. Här finns information om hur KI 
behandlar 
personuppgifter.


Sending email to Karolinska Institutet (KI) will result in KI processing your 
personal data. You can read more about KI's processing of personal data 
here.
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