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Today's Topics:
1. Re: mri_hippocampal-subfields error: MATLAB exited for no
reason (Iglesias Gonzalez, Juan E.) (Iglesias Gonzalez, Juan E.)
2. Re: Hippocampal Subfield error (Daniel Davidson Callow)
3. Re: Hippocampal Subfield error (Iglesias Gonzalez, Juan E.)
4. Re: Hippocampal Subfield error (Daniel Davidson Callow)
5. mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)
(Di?genes Bispo)
6. Group comparison with MD (Antti Cajanus)
----------------------------------------------------------------------
Message: 1
Date: Fri, 28 May 2021 19:29:14 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB
exited for no reason (Iglesias Gonzalez, Juan E.)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <7A66B3DD-56D6-4754-B9B5-84A215B1F480@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Multiple subjects or all of them?
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
> On May 28, 2021, at 12:26, ??? <ytlin923@g.ntu.edu.tw> wrote:
>
> External Email - Use Caution
>
> Dear Dear FreeSurfer Developers,
>
> (We?re the message 3)
> This happened to multiple subjects. Our computer got 16GB MHz DDR4 , We thought it met the requirements to run the module based on the documentation on freesurfer wiki , or didn?t it? :(
>
>
> Best regards,
> Josephine
>
>> freesurfer-request@nmr.mgh.harvard.edu ? 2021?5?29? ??12:03 ???
>> Send Freesurfer mailing list submissions to
>> freesurfer@nmr.mgh.harvard.edu
>>
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>> or, via email, send a message with subject or body 'help' to
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>>
>> You can reach the person managing the list at
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>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Freesurfer digest..."
>>
>>
>> Today's Topics:
>>
>> 1. (no subject) (Daniel Davidson Callow)
>> 2. Hippocampal Subfield error (Daniel Davidson Callow)
>> 3. Re: mri_hippocampal-subfields error: MATLAB existed for no
>> reason (Iglesias Gonzalez, Juan E.)
>> 4. Re: Choosing projfrac/projdist and checking mri_vol2surf
>> output (M Pope)
>> 5. Re: Hippocampal Subfield error (Iglesias Gonzalez, Juan E.)
>> 6. PVC to calculate myelin maps (Marina Fern?ndez)
>> 7. Re: PVC to calculate myelin maps (Glasser, Matthew)
>> 8. PVC to calculate myelin maps (Marina Fern?ndez)
>> 9. Re: PVC to calculate myelin maps (Glasser, Matthew)
>> 10. (no subject) (Francisca Ferreira)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 28 May 2021 07:52:44 -0400
>> From: Daniel Davidson Callow <dcallow@umd.edu>
>> Subject: [Freesurfer] (no subject)
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>> <CAFMVdsfJ9Scx1sQ+CC6BMobLtKQT6501=vTR9KKxVA4OB_rOxg@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> External Email - Use Caution
>>
>> Hello,
>>
>> I am running into errors when running
>>
>> segmentHA_T2.sh ${subj}
>> /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
>>
>> Approximately 10% of my subjects are being processed but for some reason,
>> the majority fail to execute. Here is an output from the error log.
>> ------------------------------
>> USER dcallow
>> HOST compute-4-32.bswift.umd.edu
>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
>> PROCESSID 4033
>> PROCESSOR x86_64
>> OS Linux
>> Linux compute-4-32.bswift.umd.edu
>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
>> 2.6.32-754.35.1.el6.x86_64
>> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>> ------------------------------
>>
>> #--------------------------------------------
>> #@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT
>> 2021
>> ------------------------------------------
>> Setting up environment variables
>> ---
>> INFO: error loading libraries in default configuration, trying with MCR
>> libraries only
>> LD_LIBRARY_PATH is
>> .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering
>> norm.mgz to additional volume
>> makeIsotropic WARNING: not different enough, won't reslice!
>> No more processes.
>> ERROR: could not open
>> /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
>> for reading
>> ERROR: loading
>> /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
>> as MGH
>> Warning: File
>> '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh'
>> not found.
>> [^H> In myMRIread at 64
>> In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H
>> Attempt to reference field of non-structure array.
>>
>> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211)
>>
>>
>>
>> MATLAB:nonStrucReference
>> @#@FSTIME 2021:05:27:21:39:51
>> run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61
>> P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST
>> 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
>> 31.22 29.74 28.95
>> Linux compute-4-32.bswift.umd.edu
>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
>> 2.6.32-754.35.1.el6.x86_64
>> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>>
>> T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT 2021
>>
>> I am also getting a matlab_crash_dump file
>>
>> ------------------------------------------------------------------------
>> Segmentation violation detected at Thu May 27 21:51:52 2021
>> ------------------------------------------------------------------------
>>
>> Configuration:
>> Crash Decoding : Disabled
>> Current Visual : None
>> Default Encoding : US-ASCII
>> GNU C Library : 2.12 stable
>> MATLAB Architecture: glnxa64
>> MATLAB Root : /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux
>> MATLAB Version : 8.4.0.150421 (R2014b)
>> Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29
>> 04:45:43 EDT 2020 x86_64
>> Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
>> Software OpenGL : 0
>> Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java
>> HotSpot(TM) 64-Bit Server VM mixed mode
>> Window System : No active display
>>
>> Fault Count: 1
>>
>>
>> Abnormal termination:
>> Segmentation violation
>>
>> Stack Trace (from fault):
>> [ 0] 0x00007f2b30f06213
>> /lib64/libpthread.so.0+00033299 pthread_join+00000035
>> [ 1] 0x00007f2a9f4d847d
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 2] 0x00007f2a9f4d8cac
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 3] 0x00007f2a9f5cae63
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 4] 0x00007f2a9f5af896
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 5] 0x00007f2a9f5a6b8d
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 6] 0x00007f2a9f5a6fd0
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 7] 0x00007f2a9f5aad00
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 8] 0x00007f2a9f5a5c3c
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 9] 0x00007f2a9f44fb03
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 10] 0x00007f2a9f42b9cc
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 11] 0x00007f2a9f42b132
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 12] 0x00007f2b21dcfc0a /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538
>> mexRunMexFile+00000090
>> [ 13] 0x00007f2b21dcc5c4 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00136644
>> [ 14] 0x00007f2b21dcd414 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00140308
>> [ 15] 0x00007f2b232ff329 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 16] 0x00007f2b2260fb70
>> /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
>> [ 17] 0x00007f2b225bfe02 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
>> [ 18] 0x00007f2b225c2022 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
>> [ 19] 0x00007f2b225c7f87 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
>> [ 20] 0x00007f2b225c36ff /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
>> [ 21] 0x00007f2b225c4334 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
>> [ 22] 0x00007f2b2263952e /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
>> [ 23] 0x00007f2b232ff329 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 24] 0x00007f2b2260fb70
>> /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
>> [ 25] 0x00007f2b225bfe02 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
>> [ 26] 0x00007f2b225c2022 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
>> [ 27] 0x00007f2b225c7f87 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
>> [ 28] 0x00007f2b225c36ff /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
>> [ 29] 0x00007f2b225c4334 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
>> [ 30] 0x00007f2b2263952e /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
>> [ 31] 0x00007f2b232ff329 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 32] 0x00007f2b225ecbf0
>> /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03910640
>> [ 33] 0x00007f2b225ec449 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03908681
>> [ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03137494
>> inCallFcnWithTrap+00000086
>> [ 35] 0x00007f2b225b3c0b /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03677195
>>
>> This error was detected while a MEX-file was running. If the MEX-file
>> is not an official MathWorks function, please examine its source code
>> for errors. Please consult the External Interfaces Guide for information
>> on debugging MEX-files.
>>
>> If this problem is reproducible, please submit a Service Request via:
>> http://secure-web.cisco.com/1lsmxJ1l6wT0WmnW3q7zuS6JngCO6upWHYdXR6E3TNhC0oDUsy9FhA7GwO0ghIRuurPZncG6-zhlFrAY4VY2aJReGfBN8RZTuIOU6wmDTUghXHEP5BkbyHc8_vtCBJp-zOs_fNVzEV9sMAPfYeLzVn8oHPd9KBxN7WKzCC_d6TDceaO7Lp0-BGJpb2LlY2YFIup8Is3JddKjHfPknqA7Iw6cl6zmiNI9nmeOCX8z2z7AWJIPYKzlwUwhEs6EapI5BOlXjCbd034xSGJ57pwJmrw/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
>>
>> A technical support engineer might contact you with further information.
>>
>> Any insight or help you can provide is greatly appreciated.
>> *Daniel Callow*
>> *PhD Student, Neuroscience and Cognitive Science*
>> Exercise for Brain Health Lab
>> University of Maryland, College Park
>> dcallow@umd.edu <dcallow@gmail.com>
>> 443-254-6298
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 28 May 2021 07:53:23 -0400
>> From: Daniel Davidson Callow <dcallow@umd.edu>
>> Subject: [Freesurfer] Hippocampal Subfield error
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>> <CAFMVdsc4FQTD+XGoNrrLBMjhUmK4hAG6SSPPzHxcdEFoyqEnqw@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> External Email - Use Caution
>>
>> Hello,
>>
>> I am running into errors when running
>>
>> segmentHA_T2.sh ${subj}
>> /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
>>
>> Approximately 10% of my subjects are being processed but for some reason,
>> the majority fail to execute. Here is an output from the error log.
>> ------------------------------
>> USER dcallow
>> HOST compute-4-32.bswift.umd.edu
>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
>> PROCESSID 4033
>> PROCESSOR x86_64
>> OS Linux
>> Linux compute-4-32.bswift.umd.edu
>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
>> 2.6.32-754.35.1.el6.x86_64
>> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>> ------------------------------
>>
>> #--------------------------------------------
>> #@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT
>> 2021
>> ------------------------------------------
>> Setting up environment variables
>> ---
>> INFO: error loading libraries in default configuration, trying with MCR
>> libraries only
>> LD_LIBRARY_PATH is
>> .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering
>> norm.mgz to additional volume
>> makeIsotropic WARNING: not different enough, won't reslice!
>> No more processes.
>> ERROR: could not open
>> /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
>> for reading
>> ERROR: loading
>> /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
>> as MGH
>> Warning: File
>> '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh'
>> not found.
>> [^H> In myMRIread at 64
>> In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H
>> Attempt to reference field of non-structure array.
>>
>> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211)
>>
>>
>>
>> MATLAB:nonStrucReference
>> @#@FSTIME 2021:05:27:21:39:51
>> run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61
>> P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST
>> 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
>> 31.22 29.74 28.95
>> Linux compute-4-32.bswift.umd.edu
>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
>> 2.6.32-754.35.1.el6.x86_64
>> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>>
>> T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT 2021
>>
>> I am also getting a matlab_crash_dump file
>>
>> ------------------------------------------------------------------------
>> Segmentation violation detected at Thu May 27 21:51:52 2021
>> ------------------------------------------------------------------------
>>
>> Configuration:
>> Crash Decoding : Disabled
>> Current Visual : None
>> Default Encoding : US-ASCII
>> GNU C Library : 2.12 stable
>> MATLAB Architecture: glnxa64
>> MATLAB Root : /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux
>> MATLAB Version : 8.4.0.150421 (R2014b)
>> Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29
>> 04:45:43 EDT 2020 x86_64
>> Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
>> Software OpenGL : 0
>> Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java
>> HotSpot(TM) 64-Bit Server VM mixed mode
>> Window System : No active display
>>
>> Fault Count: 1
>>
>>
>> Abnormal termination:
>> Segmentation violation
>>
>> Stack Trace (from fault):
>> [ 0] 0x00007f2b30f06213
>> /lib64/libpthread.so.0+00033299 pthread_join+00000035
>> [ 1] 0x00007f2a9f4d847d
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 2] 0x00007f2a9f4d8cac
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 3] 0x00007f2a9f5cae63
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 4] 0x00007f2a9f5af896
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 5] 0x00007f2a9f5a6b8d
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 6] 0x00007f2a9f5a6fd0
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 7] 0x00007f2a9f5aad00
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 8] 0x00007f2a9f5a5c3c
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 9] 0x00007f2a9f44fb03
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 10] 0x00007f2a9f42b9cc
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 11] 0x00007f2a9f42b132
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 12] 0x00007f2b21dcfc0a /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538
>> mexRunMexFile+00000090
>> [ 13] 0x00007f2b21dcc5c4 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00136644
>> [ 14] 0x00007f2b21dcd414 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00140308
>> [ 15] 0x00007f2b232ff329 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[
>> 16] 0x00007f2b2260fb70 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
>> [ 17] 0x00007f2b225bfe02 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
>> [ 18] 0x00007f2b225c2022 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
>> [ 19] 0x00007f2b225c7f87 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
>> [ 20] 0x00007f2b225c36ff /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
>> [ 21] 0x00007f2b225c4334 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
>> [ 22] 0x00007f2b2263952e /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
>> [ 23] 0x00007f2b232ff329 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[
>> 24] 0x00007f2b2260fb70 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
>> [ 25] 0x00007f2b225bfe02 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
>> [ 26] 0x00007f2b225c2022 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
>> [ 27] 0x00007f2b225c7f87 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
>> [ 28] 0x00007f2b225c36ff /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
>> [ 29] 0x00007f2b225c4334 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
>> [ 30] 0x00007f2b2263952e /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
>> [ 31] 0x00007f2b232ff329 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[
>> 32] 0x00007f2b225ecbf0 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03910640
>> [ 33] 0x00007f2b225ec449 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03908681
>> [ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03137494
>> inCallFcnWithTrap+00000086
>> [ 35] 0x00007f2b225b3c0b /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03677195
>>
>> This error was detected while a MEX-file was running. If the MEX-file
>> is not an official MathWorks function, please examine its source code
>> for errors. Please consult the External Interfaces Guide for information
>> on debugging MEX-files.
>>
>> If this problem is reproducible, please submit a Service Request via:
>> http://secure-web.cisco.com/1B8en4WQVOmBM-TonUpSzamw674QdqjI_ltVT2KdTcbPbuPW0K3Ay8KDhD5c4RCuwKYVmR07FjU0Aevx09ahCMeyv0JkXQ52Hmhwb4sx7s4JboH2NUrlUAj_t1NiR1NWXsdcBbrW2ARL_QZIvDtzEvCZllOY4TGkavTAZNKXychD1QqvsZFE-MKZXZcrP5pagoPPejJGw9gWjGYxJHuPexjzzMvAZ00KWwGungv_lBCKCFbVfyIShsbLN-xOO4h3eWRUjCNBh0HGJu8phyXt6Xg/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
>>
>> A technical support engineer might contact you with further information.
>>
>> Any insight or help you can provide is greatly appreciated.
>> *Daniel Callow*
>> *PhD Student, Neuroscience and Cognitive Science*
>> Exercise for Brain Health Lab
>> University of Maryland, College Park
>> dcallow@umd.edu <dcallow@gmail.com>
>> 443-254-6298
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 28 May 2021 13:20:35 +0000
>> From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB
>> existed for no reason
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <85A3C0E6-DE53-45D9-B15F-86339BF8F70D@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear Josephine,
>>
>> This is a bit weird, as the code was very close to finishing. Does this happen for one or multiple subjects? Also: is it possible that you?re running out of RAM memory? How much RAM does your computer have?
>>
>> Cheers,
>>
>> /Eugenio
>>
>> Juan Eugenio Iglesias
>> Senior research fellow
>> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>> http://secure-web.cisco.com/1SxTcd0Zo0I2s95XPEXzrpzj17CCr7JjYgYh3X8SWkG_dEY2QsgLRc4wRnT4BaPwjcBUBwXuKhijixcRZw5lmE4jv6BLKeL_Y8o1T7Bae-z46vizzPWajA_0vtXsq4m4GpTtndS2P_yw9dx4nOthYnPIGkwowjLN4GrvSqUE6m3vheLtH5I8wnG1luLMOImJ2SF2ewuXSRAJCcYUl4vYdQBGlbVcrPWcrdnRqsh8-e5wT1AHa_zP5YWb7ExWYSd6rmMxdKsQoD2ae_8-U341XZQ/http%3A%2F%2Fwww.jeiglesias.com
>>
>> On May 28, 2021, at 02:05, ??? <ytlin923@g.ntu.edu.tw<mailto:ytlin923@g.ntu.edu.tw>> wrote:
>>
>>
>> External Email - Use Caution
>>
>> Dear FreeSurfer Developers:
>>
>> We apply the hippocampal module with MATLAB R21014b runtime and FreeSurfer7.1.1, but it came up with the error:
>> MATLAB is exiting because of fatal error
>> /Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 10056 Killed: 9 /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML S029 /Applications/freesurfer/7.1.1/subjects 0.333333333333333333333333333333333333 /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 brain116deiMac.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
>>
>> We are not sure about why this happened, could you help us with this? The log file was attached for more information here. We really are grateful for your help!
>>
>>
>> Best regards,
>> Josephine
>> <hippocampal-subfields-T1.log>_______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://secure-web.cisco.com/19MxmZ-YngtXyjI8JhMif3nT9Tvss_ZmhVPTJcv7XmEmCXzu8Jy5NKIpxAAHF_M_PNz7_3o3mwUbHDADwFceLVaYl52OiJkQSu0DbKoztNgPIvgr8iPRINDSGGxfhgDXGnxZKAN9yo2NojcESoYkDDWlD8UPx0ST1HsPUowbRmRGXkPbhBAURA22d_OZqGj_UEZ-h5ZsaUL5wwI77BYUH5d_kgqMGNdhlshXSOWY6Gyd0hjEbTt_vjFR9UW0PZDouDByVW-FULZfN4r8U_gXjAA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 4
>> Date: Fri, 28 May 2021 13:25:50 +0000
>> From: M Pope <marianna.pope@hotmail.com>
>> Subject: Re: [Freesurfer] Choosing projfrac/projdist and checking
>> mri_vol2surf output
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID:
>> <PAXP192MB12166752E2BBDD875C4ECA5BFC229@PAXP192MB1216.EURP192.PROD.OUTLOOK.COM>
>>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> External Email - Use Caution
>>
>> Hi,
>>
>> Thanks for this. Using mri_surf2vol as a QC hadn't occured to me and is a nice solution. I feel again using --fillribbon is the best way to project the surface to the volume for my case?
>>
>> There is one other issue I had seen, but didn't know if it would affect my procedure. As I am examining the entorhinal cortex, it seems like part of my mask expands past the surfaces created by recon-all. I attach a screenshot of what I mean (the entorhinal mask is in yellow). When I then run mri_surf2vol, the output I get covers very well the part of my original mask that IS within the pial surfaces, but doesn't extend to include the rest of the mask. So it seems this is affecting the process.
>>
>> Do you have any suggestions as to how I can solve this issue? Would it be worth trying to reconstruct the surfaces- although they are in line with the bert subject template of freesurfer.
>>
>> Thanks,
>> Marianna
>> ________________________________
>> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
>> Sent: 27 May 2021 9:39 PM
>> To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Choosing projfrac/projdist and checking mri_vol2surf output
>>
>> If I understand you correctly, you have an ROI defined in the volume and you want to transfer it to the surface. Is that right? First you should look at the ROI in the volume along with the surfaces and make sure that they pass through the ROI. I would generally use the projfrac-max option for something like this. After you get a surface overlay, you can map it back to the volume (mri_surf2vol) and see if it looks right relative to the full volume ROI.
>>
>> On 5/21/2021 6:41 AM, M Pope wrote:
>>
>> External Email - Use Caution
>>
>> External Email - Use Caution
>>
>> Hi all,
>>
>> I have a question regarding checking the output of mri_vol2surf. I am converting a manually segmented volume ROI into a surface label in order to gain information such as cortical thickness.
>> What is the best practice for quality control and checking the surface rendering of the ROI? Are there any protocols or suggestions? As slight changes in projfrac change the output by a large degree, it's difficult to assess what is the closest to the original volume ROI. The suggestions also vary (others say projfrac 0.5, others to use projfrac-max or projdist). The main output statistic I'm interested in cortical thickness of the region (if this influences the options).
>>
>> How do you choose and establish what is the best option?
>>
>> Thanks
>> Marianna
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://secure-web.cisco.com/1crndCNiNtoGVMPUhoNnIxDSbZaX5xv97bIlJ1N0pCUII7EcUVI4slR0gbGN3F62lLnTmj7wr-dJaeO9AKmBNBMeRzatolyfg2XS1XoFHeDuVU1n5eI0HQGrT2PoZZ_VYiryY1YhhJbsD-EUTUlMW_2tw6yWS3nTlcCuYS6XJUtsKSnQimsZ_ul5RXOMaKs2vYbC7LZ7Y20VR6b01z1Akn0G73LdPu-zgYWeS1aWy8RoC9O8ATX7WyQMimsPJ-iBV5-5ynzL01HECR1yfmCIn5Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>
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>> Size: 47906 bytes
>> Desc: ec-mask-surface.png
>> Url : http://secure-web.cisco.com/1ZLELUyV23_PjRQVZfoG7a58LZcp9kOqeMcvQ5wTFfZzO13HB9etxHEwn2flgR0KmrmnQov82C910e-5ItwFrJxv37bcEKpvYEBtREi_k1bFg4F-l4icf5AbCr9md-rAAtYMDLhLO3iPDi8SjHdSDry_wB2yyAX98baktBpoLH7vVKQGisaa1vQnkRQjQ_I9OHpp3ZLffIqjsfZXhvTPDdMBTcOd6LZrY5ujpmXz-YXnlsP_Twi_ubykCjkN5brXOCNCQDVF3SOQZ6rEQ_TStBg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210528%2F66676285%2Fattachment-0001.png
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Fri, 28 May 2021 13:31:51 +0000
>> From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Hippocampal Subfield error
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <316477CD-FAAB-4FE5-AA26-5A4D312C5247@mgh.harvard.edu>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Dear Daniel,
>>
>> Are the T2s and T1s roughly aligned in RAS (physical coordinates)? In other words: do they (roughly) overlap when you open them together in Freeview?
>>
>> Cheers,
>>
>> /E
>>
>> Juan Eugenio Iglesias
>> Senior research fellow
>> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>> http://secure-web.cisco.com/1SxTcd0Zo0I2s95XPEXzrpzj17CCr7JjYgYh3X8SWkG_dEY2QsgLRc4wRnT4BaPwjcBUBwXuKhijixcRZw5lmE4jv6BLKeL_Y8o1T7Bae-z46vizzPWajA_0vtXsq4m4GpTtndS2P_yw9dx4nOthYnPIGkwowjLN4GrvSqUE6m3vheLtH5I8wnG1luLMOImJ2SF2ewuXSRAJCcYUl4vYdQBGlbVcrPWcrdnRqsh8-e5wT1AHa_zP5YWb7ExWYSd6rmMxdKsQoD2ae_8-U341XZQ/http%3A%2F%2Fwww.jeiglesias.com
>>
>> On May 28, 2021, at 07:53, Daniel Davidson Callow <dcallow@umd.edu<mailto:dcallow@umd.edu>> wrote:
>>
>>
>> External Email - Use Caution
>>
>> Hello,
>>
>> I am running into errors when running
>>
>> segmentHA_T2.sh ${subj} /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
>>
>> Approximately 10% of my subjects are being processed but for some reason, the majority fail to execute. Here is an output from the error log.
>> ------------------------------
>> USER dcallow
>> HOST compute-4-32.bswift.umd.edu<http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
>> PROCESSID 4033
>> PROCESSOR x86_64
>> OS Linux
>> Linux compute-4-32.bswift.umd.edu<http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu> 2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>> ------------------------------
>>
>> #--------------------------------------------
>> #@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT 2021
>> ------------------------------------------
>> Setting up environment variables
>> ---
>> INFO: error loading libraries in default configuration, trying with MCR libraries only
>> LD_LIBRARY_PATH is .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering norm.mgz to additional volume
>> makeIsotropic WARNING: not different enough, won't reslice!
>> No more processes.
>> ERROR: could not open /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh for reading
>> ERROR: loading /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh as MGH
>> Warning: File '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh' not found.
>> [^H> In myMRIread at 64
>> In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H
>> Attempt to reference field of non-structure array.
>>
>> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211)
>>
>>
>>
>> MATLAB:nonStrucReference
>> @#@FSTIME 2021:05:27:21:39:51 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61 P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 31.22 29.74 28.95
>> Linux compute-4-32.bswift.umd.edu<http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu> 2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>>
>> T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT 2021
>>
>> I am also getting a matlab_crash_dump file
>>
>> ------------------------------------------------------------------------
>> Segmentation violation detected at Thu May 27 21:51:52 2021
>> ------------------------------------------------------------------------
>>
>> Configuration:
>> Crash Decoding : Disabled
>> Current Visual : None
>> Default Encoding : US-ASCII
>> GNU C Library : 2.12 stable
>> MATLAB Architecture: glnxa64
>> MATLAB Root : /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux<http://secure-web.cisco.com/1zf_ot3cQGUvMhTgphfJ7towMivhNxWKqA3AayyU_OPHHiMasb-EvBGTFN3sYYJDfq2OTyGKzBZ_szFAJCXZHlZGEtJjl-Jdhb4Q1bIAonDtiewkPoyMXUpsAcQaKfsBE0RsmUc-YGdemu96LMj476x2UIb3GfDNjDVx7ULnA6ydsfS5RHTfxedRiKFt6oLIZ-8AmzrNc44dziwIEz2Tm1zVXkZba_ISfg8fwql2KxoL8WGjCE7_3XIDrEbE-HNmMPhnNu3asRalw0_AJ6BOTkA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux>
>> MATLAB Version : 8.4.0.150421 (R2014b)
>> Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64
>> Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
>> Software OpenGL : 0
>> Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
>> Window System : No active display
>>
>> Fault Count: 1
>>
>>
>> Abnormal termination:
>> Segmentation violation
>>
>> Stack Trace (from fault):
>> [ 0] 0x00007f2b30f06213 /lib64/libpthread.so.0+00033299 pthread_join+00000035
>> [ 1] 0x00007f2a9f4d847d /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 2] 0x00007f2a9f4d8cac /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 3] 0x00007f2a9f5cae63 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 4] 0x00007f2a9f5af896 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 5] 0x00007f2a9f5a6b8d /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 6] 0x00007f2a9f5a6fd0 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMat
lab
>> .mexa64+0$[ 7] 0x00007f2a9f5aad00 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 8] 0x00007f2a9f5a5c3c /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 9] 0x00007f2a9f44fb03 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 10] 0x00007f2a9f42b9cc /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 11] 0x00007f2a9f42b132 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 12] 0x00007f2b21dcfc0a /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538<http://secure-web.cisco.com
/1
>> 5wmunFtJy8RzDq9oVQoOhvMj4SqFWIMICnRxUk7kN3uy!
>> Ytej40W1
>> KAf2FgN8p-YHhCe94AM96CLuzs2_pg0h5a-wPhOcAbQDBbn9UroNugqM9zMNW_x85lUFfPpgR5eVTK_sVWwcg4CiDnJkgZm34QYRBZBTcAYN9riNJ9m1rpj4PKAxhbRXEmUfM_1qcroQ-tCUoHaYthJ1wh2oe_rXJu65oN57rZkO5uN2D-kO6NX50rAL6N-yYqFbQTvlWSoqZXcpaDvh0nH11oRbZSCgYQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmex.so%2B00150538> mexRunMexFile+00000090
>> [ 13] 0x00007f2b21dcc5c4 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00136644<http://secure-web.cisco.com/1VNIP2TP7g_-k-V3EXmoqH3gSLCQPAVKDrJmmFHk4DSCIs8dpaPhlMZY3o1R2Gcl45b59huNzCHAuDXy3Jk_DTzSHWeoAdTGEyyL_kxblZnIJkrmRuC21lPT3uRUUA5F-hhCNI4L1ewaawelx52Ns4n9o9ra_oWhRf9AD84pTyjJnXGVX1FrlCKhr8xCI3BxucHGenwthYaUBlmin56HnLgin-otSEMgaMDZVIlfwdsJjpm_sB9ATY4IgK9GI4jaKI7g9MMLbHjEVqHgacPW6sw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmex.so%2B00136644>
>> [ 14] 0x00007f2b21dcd414 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00140308<http://secure-web.cisco.com/1DHyyF-k0XGkPk9gRiFdvyrzyhAwZmrJ8Vpas5l1bhBSmDpXf1DE5cQ_3mHR9xgFvggvUyK6nS-KPKUap_Y3PtkQxvO-b174nhgWgkAkhqF0GCz9M2ffTgT-YPppDR2yc8dr-rFkMth1BYS8tXsV0l1UcZ8aP_QkA_xu_XEQ-IULq2naXsfdbIOmnONEUC_6gpFEpp2_EkJr0prYDw63-Fcx2DNkGKP9H_lYz9w8au_3bwu-8Upbm2dSza-8ykxGxxKbsp1J3VugjWqfirkKTxg/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmex.so%2B00140308>
>> [ 15] 0x00007f2b232ff329 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337<http://secure-web.cisco.com/1YvAiBC_3G9VAawE4steKXeCaNTlrpgMnQG_qhwLeycblS635IsShf_UEZVAtvWU98ic7nFoyTObuenzWyfIOrdZ1ukAI2_Rwpr7BFODPD8xr8FVnAIglj8lndurD-18acdOLCAx9cl__2Xe2_21LZQn4auLKXubsYP6cvn7ODCEtX6tup_3H0vUFEZ4WQGRknJISa7pBZBc8A0cMb8ooCFDVafzDFjkSj4EiKd-9hl01YeUQPAu5Hwt6s7FUSKNmxksu_SyBfaeCpYE8OvqpHA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_dispatcher.so%2B00791337> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 16] 0x00007f2b2260fb70 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872<http://secure-web.cisco.com/1FqlnK1mbYe0fc4WrLh27McIgFcpF4caZpprfvWHGIiLLoxXo6_L3M8BINfHY5-jSh1ngRLTREAlaV-ecKWLXgaZmAvPaE1WcZ3K8NB0Vvxh-3_asNJndl8j3D5yqTCWCZygCAlsQE2BScTJzzzgOg0nDdICKmBjoe5NmIpTDU8e12QBMlVY4gLY59bk2WU5NEVeEhnmukrN_bzXIchegVXLsx6fumnKQzIoSHTfUwa7LAM4D8pzDWBH
7hs
>> RyezlzADNhYYUpmOqNOqn5JFOEDA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04053872>
>> [ 17] 0x00007f2b225bfe02 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850<http://secure-web.cisco.com/1oFCMQbMq8_LNNSwavId3uL9KorlKBV-Dq9AH2k9--Ptuwe56v1f0M8oNm9UBgRvAQacl9RKg1Qg0DY7ko-IcvfQe-2sfN0qRBoXdPr8AINOFM5HQFjasYlRzdVlc-G_JqKNPbJEzsVRjfXLn9CA4BIE2htjH6A3_wsQTimZoAzJF_HNTmhJ7qA5E1fFaDN7kOubeJKvBSvnuTwu-bMBUREZA03ALLxwcXdU7Zf9awXp32KrUJr3sssPhgqjOZm0-uLmk2eWzYlnYg6SD7XCpag/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03726850>
>> [ 18] 0x00007f2b225c2022 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586<http://secure-web.cisco.com/1mkHocgN-E2JcT6SI0pNs-oXMVy5k5oGB6gATPm9NI82pijbaPsiS_mVu6yD_8ldltWLoJH4dyPp4vYVPvfXnMD03lmxENx9NH-5f5d00CK147UzH945ZVfrdnKRmxtQZPQAbtHNrwjMC7s4lNIqHSR7GSaetK6V29YMKzu_-Tu1SwwBDg3JePYZjvodQRdYUkHEfs8YmahPAtNRQPM3MskmCOUcjL4tV6sdY1yfjwhrpmPrjlQKVXgKZQMDqosdS_VLmyb6B_maYrhrDgnW0aA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03735586>
>> [ 19] 0x00007f2b225c7f87 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007<http://secure-web.cisco.com/1IXEh5f9oNhkKzllddjiYB3PrZZ0_a0EZYlGzFTPY7IyKerNHNEwXaFMOYZXMm4hct0Rom3hL_ou_TGy8UJSc7P-OrfKK0CrXSeDSR-7YEwoHUr9hq-a_cceHo-B4JS3oLxWaU0ykCPBleBOrFVoTgQHmHnKJTjxDY5GAIqCi48jEIy7iuEXH8AMIgvxL5dbjDgjN_qtXvhWG70-bIbaIS0j25znSUF0ho6j9W7Q-okSGwCZJ0YkWBJerVuCH5b3o_Rr2u-KSeDxXNKED0dtlBw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03760007>
>> [ 20] 0x00007f2b225c36ff /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439<http://secure-web.cisco.com/1z7kRHrPDXQ2J89IxYNotG6f3AWl-VlFzlspUBbkrsL1gDgJbVg7Jvui01VXzy_9XgOLBM7uiNrNy2emqwnaZRVr97UmD81gSG0_F-eUpsqBkSrR3o5bOkcSlKSKbnIJLwrb7IlUi1lGu-eqqDsDfvtd8bmEZ9LWhsNqU63v-ByjHg8-Tppp8IHXCegbHJwtiYG5b7ldmmACZL3zXlOMT5m_Xf7vUxnL9hQ9AOVduNe9rwSJml83zaACIYRO7148iHaaWASzcChMIFktUQdn6DA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03741439>
>> [ 21] 0x00007f2b225c4334 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564<http://secure-web.cisco.com/1Qidv5KKgCpV0A4yNcjeOaCG5BbPEneNCG_VGPSEeihppLC0K8VCKQKqgycrF_JG7hDWxESiIkJ0zZSKIoEcr9MBBq-zCjGrXAT3o-uxNgPfkPx2Diq5rB4I4Nj_5SOHSz67iis8FUiswPfla7T1ax5dsZbZqWNZzf3mRlN9H7qfLp7x9gNQlbo1DsK8hFvHTUGz_PM_4onSpO9CffOK0BfVEfeOpXOHy6EjznUeUWhuJyx6dorWoftGwaDXEKw44ZGcYPHdtnJXKpRfHp8TKpw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03744564>
>> [ 22] 0x00007f2b2263952e /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302<http://secure-web.cisco.com/1LFwdsCWta1IKYv3k3YydtSX7z6ZkdwRsguf-SFigI8Kxt4X2FK9QjJHavPcu2kTMH1M8_iHldk2sCDW-6Cw6fokp46WGvsOCfyh25z_jqednT1Bw_Rij1zigZ9QCabcdCHHrRmXYLySPYEVnuaTn22efOadhUo6Nk4TlR0yJ9IkLdzQFrQh_3bCoEoX8T_dZVAmOpLbfqeCTnXHh06TvfZx3I9xWFZvsuURivUTNG_DPyZpHm1y05pMXl4mY_b6ff5sdtFbOIGeh7kop0ZDDEw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04224302>
>> [ 23] 0x00007f2b232ff329 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337<http://secure-web.cisco.com/1YvAiBC_3G9VAawE4steKXeCaNTlrpgMnQG_qhwLeycblS635IsShf_UEZVAtvWU98ic7nFoyTObuenzWyfIOrdZ1ukAI2_Rwpr7BFODPD8xr8FVnAIglj8lndurD-18acdOLCAx9cl__2Xe2_21LZQn4auLKXubsYP6cvn7ODCEtX6tup_3H0vUFEZ4WQGRknJISa7pBZBc8A0cMb8ooCFDVafzDFjkSj4EiKd-9hl01YeUQPAu5Hwt6s7FUSKNmxksu_SyBfaeCpYE8OvqpHA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_dispatcher.so%2B00791337> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 24] 0x00007f2b2260fb70 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872<http://secure-web.cisco.com/1FqlnK1mbYe0fc4WrLh27McIgFcpF4caZpprfvWHGIiLLoxXo6_L3M8BINfHY5-jSh1ngRLTREAlaV-ecKWLXgaZmAvPaE1WcZ3K8NB0Vvxh-3_asNJndl8j3D5yqTCWCZygCAlsQE2BScTJzzzgOg0nDdICKmBjoe5NmIpTDU8e12QBMlVY4gLY59bk2WU5NEVeEhnmukrN_bzXIchegVXLsx6fumnKQzIoSHTfUwa7LAM4D8pzDWBH
7hs
>> RyezlzADNhYYUpmOqNOqn5JFOEDA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04053872>
>> [ 25] 0x00007f2b225bfe02 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850<http://secure-web.cisco.com/1oFCMQbMq8_LNNSwavId3uL9KorlKBV-Dq9AH2k9--Ptuwe56v1f0M8oNm9UBgRvAQacl9RKg1Qg0DY7ko-IcvfQe-2sfN0qRBoXdPr8AINOFM5HQFjasYlRzdVlc-G_JqKNPbJEzsVRjfXLn9CA4BIE2htjH6A3_wsQTimZoAzJF_HNTmhJ7qA5E1fFaDN7kOubeJKvBSvnuTwu-bMBUREZA03ALLxwcXdU7Zf9awXp32KrUJr3sssPhgqjOZm0-uLmk2eWzYlnYg6SD7XCpag/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03726850>
>> [ 26] 0x00007f2b225c2022 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586<http://secure-web.cisco.com/1mkHocgN-E2JcT6SI0pNs-oXMVy5k5oGB6gATPm9NI82pijbaPsiS_mVu6yD_8ldltWLoJH4dyPp4vYVPvfXnMD03lmxENx9NH-5f5d00CK147UzH945ZVfrdnKRmxtQZPQAbtHNrwjMC7s4lNIqHSR7GSaetK6V29YMKzu_-Tu1SwwBDg3JePYZjvodQRdYUkHEfs8YmahPAtNRQPM3MskmCOUcjL4tV6sdY1yfjwhrpmPrjlQKVXgKZQMDqosdS_VLmyb6B_maYrhrDgnW0aA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03735586>
>> [ 27] 0x00007f2b225c7f87 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007<http://secure-web.cisco.com/1IXEh5f9oNhkKzllddjiYB3PrZZ0_a0EZYlGzFTPY7IyKerNHNEwXaFMOYZXMm4hct0Rom3hL_ou_TGy8UJSc7P-OrfKK0CrXSeDSR-7YEwoHUr9hq-a_cceHo-B4JS3oLxWaU0ykCPBleBOrFVoTgQHmHnKJTjxDY5GAIqCi48jEIy7iuEXH8AMIgvxL5dbjDgjN_qtXvhWG70-bIbaIS0j25znSUF0ho6j9W7Q-okSGwCZJ0YkWBJerVuCH5b3o_Rr2u-KSeDxXNKED0dtlBw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03760007>
>> [ 28] 0x00007f2b225c36ff /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439<http://secure-web.cisco.com/1z7kRHrPDXQ2J89IxYNotG6f3AWl-VlFzlspUBbkrsL1gDgJbVg7Jvui01VXzy_9XgOLBM7uiNrNy2emqwnaZRVr97UmD81gSG0_F-eUpsqBkSrR3o5bOkcSlKSKbnIJLwrb7IlUi1lGu-eqqDsDfvtd8bmEZ9LWhsNqU63v-ByjHg8-Tppp8IHXCegbHJwtiYG5b7ldmmACZL3zXlOMT5m_Xf7vUxnL9hQ9AOVduNe9rwSJml83zaACIYRO7148iHaaWASzcChMIFktUQdn6DA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03741439>
>> [ 29] 0x00007f2b225c4334 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564<http://secure-web.cisco.com/1Qidv5KKgCpV0A4yNcjeOaCG5BbPEneNCG_VGPSEeihppLC0K8VCKQKqgycrF_JG7hDWxESiIkJ0zZSKIoEcr9MBBq-zCjGrXAT3o-uxNgPfkPx2Diq5rB4I4Nj_5SOHSz67iis8FUiswPfla7T1ax5dsZbZqWNZzf3mRlN9H7qfLp7x9gNQlbo1DsK8hFvHTUGz_PM_4onSpO9CffOK0BfVEfeOpXOHy6EjznUeUWhuJyx6dorWoftGwaDXEKw44ZGcYPHdtnJXKpRfHp8TKpw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03744564>
>> [ 30] 0x00007f2b2263952e /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302<http://secure-web.cisco.com/1LFwdsCWta1IKYv3k3YydtSX7z6ZkdwRsguf-SFigI8Kxt4X2FK9QjJHavPcu2kTMH1M8_iHldk2sCDW-6Cw6fokp46WGvsOCfyh25z_jqednT1Bw_Rij1zigZ9QCabcdCHHrRmXYLySPYEVnuaTn22efOadhUo6Nk4TlR0yJ9IkLdzQFrQh_3bCoEoX8T_dZVAmOpLbfqeCTnXHh06TvfZx3I9xWFZvsuURivUTNG_DPyZpHm1y05pMXl4mY_b6ff5sdtFbOIGeh7kop0ZDDEw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04224302>
>> [ 31] 0x00007f2b232ff329 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337<http://secure-web.cisco.com/1YvAiBC_3G9VAawE4steKXeCaNTlrpgMnQG_qhwLeycblS635IsShf_UEZVAtvWU98ic7nFoyTObuenzWyfIOrdZ1ukAI2_Rwpr7BFODPD8xr8FVnAIglj8lndurD-18acdOLCAx9cl__2Xe2_21LZQn4auLKXubsYP6cvn7ODCEtX6tup_3H0vUFEZ4WQGRknJISa7pBZBc8A0cMb8ooCFDVafzDFjkSj4EiKd-9hl01YeUQPAu5Hwt6s7FUSKNmxksu_SyBfaeCpYE8OvqpHA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_dispatcher.so%2B00791337> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 32] 0x00007f2b225ecbf0 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03910640<http://secure-web.cisco.com/1XY2HS1eoFmCZj_0FLnEggB0qkNY41bJhNhIxrQkYQlfUUFOeH7A1s1kvm8DQWM0JlgCJOvl0vJiumfWqWZpNqcPopcWLIVMrGP89FTG4LxSpueiRrp0XpSeQ-vDq_Gp62up2g5nwwIVcmd7-oGNZmWQzFkkViXG0-KZbB3pU0t5L9QDBRtqK8nLjqVkLlKjqncDvdWTxmejTP9mpEj20zQuBbn_-88xbgdpbszqvtvKEThIjeHxG57d
1Se
>> K3JuQLoJ9FFtxjVfLmaIa15EmzgQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03910640>
>> [ 33] 0x00007f2b225ec449 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03908681<http://secure-web.cisco.com/15RN_eXEIUAO_WqqYNIIAMljnNJvT34HmTcfAnwdPgjQ5Zs_ljlxOt3x13LTRvM7d5IunUlOUz5aKZ7GubCOSwKdOyfM_N8vvu2s8rcvMi_VSMoOHrf9PjqE-VmSGbzKW0i_9a6AXA6ZDjAeKelV7RTipDEECT6fzvwMMYPf94nguZ7fEEF4bMoM2nZHkvhvuZGI_ZTO8PGtiq5ntFL907fj7pH9SWOuz8Nk9t5X7rPPQ0ntQShuBYa89QKVU2cfmhQRoAogbmYs22gLetkR8ZQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03908681>
>> [ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03137494<http://secure-web.cisco.com/1XibXIDoYPELJ8Qmp8ylDzLuf8aUubO7-jyooiQCEf8a082UlM2DJiqW5LaFdKT1yQJbxTKlXm1N_dBVMT-orB0SEIbRxWaLJDGWLozzZ8D-UhNRaYXYgWHAzjvA6draUI0HwfhbOmcDglBW0Q06X4mOA2cCvheWHU-rDg5mA3PdplDBSiG6JmbgZg-feiB947xEiq2BUD8ZrJe9j8XTPhjYBed6n1I_4WbG9tNT1YNCCpzNtFjBtVwnO-NTCN4QbXB2UmoKnv8og7_XILbQrEg/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03137494> inCallFcnWithTrap+00000086
>> [ 35] 0x00007f2b225b3c0b /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03677195<http://secure-web.cisco.com/1IAIH2i6-h19TW-GQXcC6sE7doC05sQYZagDqPgNU7ylypApwktFIOYKOoaKDLZKVt6j1FAmWztWJ2TpLtqqgQ_JPtZUaeDVOLW6CQR7hI9SuV0fizRPOBwBdGUHvBvKq2W35Tmj27nCuylilBfvIx_fAJmYZvwD8WFgDdLEl4sZmL812gt0QLdUyaJa5Av3bXoLMpCjFcB1nM8CY9SVYRn98cmJyTHQ5hRsVF0m8j3uzDgGf6cW5wRbtzDfQ2RQG8zgWtA8CAoUH_oMeziILfA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03677195>
>>
>> This error was detected while a MEX-file was running. If the MEX-file
>> is not an official MathWorks function, please examine its source code
>> for errors. Please consult the External Interfaces Guide for information
>> on debugging MEX-files.
>>
>> If 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://secure-web.cisco.com/1RvpYo_KUxMsoqGtxWF487Ujosracu_GU_7pOuzpwYcq1h9RXBASzcaB7NEmz8BqmzivB2D5yyk4-e6KhR9JkaOX7eSo6P4mQGbmYWY7xS4VI8fLw2Yj-dDuOiOlvrkJ4QwM1YVTI6iNH907wiJUBlMkjVZbyS7jvjHgfx_vcRAs2TqwQJ0_oPceAaqdRy-ltd7xotswU_fJi1c2NHy9iRxdF0Ree7baNS1ga1gkXUQwSBtRaeacBxyaZ4VbwAwS8n0cysGqcgwNgLmruk888kw/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F<http://secure-web.cisco.com/1B8en4WQVOmBM-TonUpSzamw674QdqjI_ltVT2KdTcbPbuPW0K3Ay8KDhD5c4RCuwKYVmR07FjU0Aevx09ahCMeyv0JkXQ52Hmhwb4sx7s4JboH2NUrlUAj_t1NiR1NWXsdcBbrW2ARL_QZIvDtzEvCZllOY4TGkavTAZNKXychD1QqvsZFE-MKZXZcrP5pagoPPejJGw9gWjGYxJHuPexjzzMvAZ00KWwGungv_lBCKCFbVfyIShsbLN-xOO4h3eWRUjCNBh0HGJu8phyXt6Xg/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F>
>>
>> A technical support engineer might contact you with further information.
>>
>> Any insight or help you can provide is greatly appreciated.
>> Daniel Callow
>> PhD Student, Neuroscience and Cognitive Science
>> Exercise for Brain Health Lab
>> University of Maryland, College Park
>> dcallow@umd.edu<mailto:dcallow@gmail.com>
>> 443-254-6298
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://secure-web.cisco.com/19MxmZ-YngtXyjI8JhMif3nT9Tvss_ZmhVPTJcv7XmEmCXzu8Jy5NKIpxAAHF_M_PNz7_3o3mwUbHDADwFceLVaYl52OiJkQSu0DbKoztNgPIvgr8iPRINDSGGxfhgDXGnxZKAN9yo2NojcESoYkDDWlD8UPx0ST1HsPUowbRmRGXkPbhBAURA22d_OZqGj_UEZ-h5ZsaUL5wwI77BYUH5d_kgqMGNdhlshXSOWY6Gyd0hjEbTt_vjFR9UW0PZDouDByVW-FULZfN4r8U_gXjAA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>
>> -------------- next part --------------
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>> URL: http://secure-web.cisco.com/1foFgPyajBvErqLM1uYstIzCPpo3BfvUv2w6mo6pfCiz1i4Ml0hj5H0TAigKFMO1iCL_uR6fGmTz-roQQNQzyaiWjhKXLCzzGmL9m1coOL4ZL7NRqMDbDQPhjS8Tiq-4MMklytBUlFnqnJni1159j4zsdvN-2tJafXTXGRR6NfRyRlvUWzU6Uf8WZhyUe_1ss4WJRwmiXAFwZA8n4HQ4AoZKv73kBVqSyyFyvxuYBGgT0ScS4FdU-zZu4kSROX6k8JbK4mBh0COT0eKSCGloGjA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210528%2F8f29ef3d%2Fattachment-0001.html
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Fri, 28 May 2021 16:25:33 +0200
>> From: Marina Fern?ndez <marina.fdez.alvarez@gmail.com>
>> Subject: [Freesurfer] PVC to calculate myelin maps
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>> <CAALjZmdoC=7LGupk0zSPrsSxN7Zao9+F=5zLRqAGoZM_Dqcc3w@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> External Email - Use Caution
>>
>> Dear experts,
>>
>> I want to calculate myelin maps using the ratio of T1w and T2w MRI images.
>> I saw that the correction of partial volume effects can be used to create
>> the maps (Shafee, Buckner & Fischl, 2015)*.
>>
>> Can I use the PVC functions of PetSurfer for this purpose? And in case I
>> can:
>>
>> Should I apply PVC only on T1? Or also in T2?
>>
>> Which T1 should I use? The original T1 or the T1 with corrections (for
>> example, the nu.mgz file that is corrected for variations in intensity)?
>>
>> Any other advice for calculating myelin maps would be welcome.
>>
>> Thank you in advance,
>>
>> Marina
>>
>>
>> *Link:
>>
>> https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ5T86whDDL8Q-4ZOYG7rMgwoBYIyC4d5BsThH9nR2UT-_82NU3WKyCZrii6txF4QxCWh-K6Hy6aC2vsOwRupJhTnA_Menjtq1hXOSwjndsWxN3BBnw625eBs0OgB8t1ZM0uY7sLR_VuAuMcsvNsQQ9qofNHMaLp6aidYJh3yhta2kwGeWzCXmtyE1XOS-Z2uiDZa5gqmp9A0egHtAOC68aEN1v8l0S-ikEhif20Qg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: http://secure-web.cisco.com/1WNjH-zk-34jNZ7tv8jku6YiQV1vcQ1P8xiTFmxC_dY8qdG4RQdQv31NzJyJuyl2IDyobu4pNMdirVquTJNhmF44Iwo0p0AzY5fEieCTdFF5SVLYun-YiBGw8m-2gnxb3jC2Rude5wZ2ALYGQA3toJOBIGE71W8wzZXljLImxslF0evjgOsvhruX-XGRHWr40VBbqaVdI02_W0t0GRYDhha_F31K0_KbNN0fhqZgDzhaKk_FoSbzlRXt9Vsn7NKDgIadya5P6_hCBYxE0_W5GMQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210528%2Fdf4153a1%2Fattachment-0001.html
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Fri, 28 May 2021 14:33:16 +0000
>> From: "Glasser, Matthew" <glasserm@wustl.edu>
>> Subject: Re: [Freesurfer] PVC to calculate myelin maps
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <0E0C0BB2-D0CB-4ED9-AF3C-CE5FBFFD2593@wustl.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> External Email - Use Caution
>>
>> I would use the HCP Pipelines for this.
>>
>> Matt.
>>
>> From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Marina Fern?ndez <marina.fdez.alvarez@gmail.com>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Friday, May 28, 2021 at 9:25 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Subject: [Freesurfer] PVC to calculate myelin maps
>>
>>
>>
>> External Email - Use Caution
>> Dear experts,
>>
>> I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I saw that the correction of partial volume effects can be used to create the maps (Shafee, Buckner & Fischl, 2015)*.
>> Can I use the PVC functions of PetSurfer for this purpose? And in case I can:
>> Should I apply PVC only on T1? Or also in T2?
>> Which T1 should I use? The original T1 or the T1 with corrections (for example, the nu.mgz file that is corrected for variations in intensity)?
>> Any other advice for calculating myelin maps would be welcome.
>> Thank you in advance,
>> Marina
>>
>> *Link:
>> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1u63hhRf89DUCFEbAiJgcglonczMMzDanUvnXz0DR2W2P39ddbeTTd8zOdP-ChfOveA6XCFA9OL0oSXezE1e96Zfb3KxYR2LDlW-jMoaOoDyQzXJ1Go8H55H3p9wb-PUnVAgkSARhLETfdcQE1Jy3gqRrJtBfJp0CHVh3heFHtl4qp4F98--n6sY0supjb4IKVTOS7yXscz0-PWIge3FA_BDxgUHKOMICIqgiNYDKcVpC3Hr1WYj-GctL7TMtCW-fB7qAj4t3Gaf-ErOb_DKx5g/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48<https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ5T86whDDL8Q-4ZOYG7rMgwoBYIyC4d5BsThH9nR2UT-_82NU3WKyCZrii6txF4QxCWh-K6Hy6aC2vsOwRupJhTnA_Menjtq1hXOSwjndsWxN3BBnw625eBs0OgB8t1ZM0uY7sLR_VuAuMcsvNsQQ9qofNHMaLp6aidYJh3yhta2kwGeWzCXmtyE1XOS-Z2uiDZa5gqmp9A0egHtAOC68aEN1v8l0S-ikEhif20Qg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48>
>>
>> ________________________________
>> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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>>
>> ------------------------------
>>
>> Message: 8
>> Date: Fri, 28 May 2021 17:06:42 +0200
>> From: Marina Fern?ndez <marina.fdez.alvarez@gmail.com>
>> Subject: [Freesurfer] PVC to calculate myelin maps
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>> <CAALjZmf4pFnh74GC+3JZJ0H9cckW43D-UT9gi+OYVzy6Kug+qA@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> External Email - Use Caution
>>
>> Hi Matt,
>>
>> Thank you very much for the quick answer.
>>
>> We have our data analyzed with another pipeline that also uses Freesurfer
>> functions. For this reason we prefer to calculate myelin maps outside of
>> the HCP Pipelines.
>>
>> Do you think the way of calculating the maps that I explained in the
>> previous question is evenly valid?
>>
>> Best wishes,
>> Marina
>>
>>
>>
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>>
>> Glasser, Matthew
>> <https://secure-web.cisco.com/1EkIb4RUBbvp4aaCzTKvZqXi5mpWtbK6dEiwb2GFTBe5yhOUyifO_hV_E7W1QbzRQK0FwD5cE3KcRI74D3Ovox656ePedxamjtVAEW4AgL4A-7CpFTGP6z5Tq41NoOZ1ojD9zFUJk5ThErtAOajuSKZWvKvti9tqMIHF1q6hCwGlKHevaGmbXlNhh9Qy7R3bO5NIgNuF-fVDEzMvEnu0zjfgN_OsOBclQQKnAUOgbQN0YXzNIZrmOblbk3L2t_TpeCz4wAM71ypty2rwIPsMJYA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Glasser%252C%2BMatthew%2522>
>> Fri, 28 May 2021 07:34:15 -0700
>> <https://secure-web.cisco.com/1ljnBFwkQWFVBlnoXgh6utmDhvf7eskDl5mAoznGoGHO9FTeVRUYQtO-bfot3HqDYDehtfxbJhabnlcLwYGpH0dXP12Y55bVR65aMaKLBI2m5e3DpuIaGvkf3ceK3XJu0-ejvTaS0490ojIjr2iIxgGPOUX8HzFmINOe0OqACHWQa_U11JZn92WpectdOwu7kUNnLEJ1EEOKgypAFQnxBzkuHv-Esidv8bS9Fwbh--pHmipQ4dKxzOK4XeRnn2fte3bTthJQyxPdc-hxBj4-oqg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210528>
>>
>> External Email - Use Caution
>>
>> I would use the HCP Pipelines for this.
>>
>> Matt.
>>
>>
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> Marina Fern?ndez
>> <https://secure-web.cisco.com/1jnEmX8pyslFDNAKq1ESVKhaVYgavR5DWrZDCQVw6EIjIeRPu8VsMW2BmjjGD5q-TEhUnOvxdrLSTT5-Y6k0YXgDL7svI9z3nYXjvFbLZ7RTupBSGPm81_9ITZGgKJJOgPJdln72nUn8_i_M0BwX5vAQJhvU59P4tJ425dDyWnDLjXoT8Isqf8qqqez-ioXBS40q0Uny8MDDL0kBndUynxMfDLd8eLFxK2zhH_m6k3AE0fJN7n9AYbodo3QU0dDBjU5tlYbAcURsJL_uHxBtJ5Q/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Marina%2BFern%25C3%25A1ndez%2522>
>> Fri, 28 May 2021 07:26:19 -0700
>> <https://secure-web.cisco.com/1ljnBFwkQWFVBlnoXgh6utmDhvf7eskDl5mAoznGoGHO9FTeVRUYQtO-bfot3HqDYDehtfxbJhabnlcLwYGpH0dXP12Y55bVR65aMaKLBI2m5e3DpuIaGvkf3ceK3XJu0-ejvTaS0490ojIjr2iIxgGPOUX8HzFmINOe0OqACHWQa_U11JZn92WpectdOwu7kUNnLEJ1EEOKgypAFQnxBzkuHv-Esidv8bS9Fwbh--pHmipQ4dKxzOK4XeRnn2fte3bTthJQyxPdc-hxBj4-oqg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210528>
>>
>> External Email - Use Caution
>>
>>
>> Dear experts,
>>
>> I want to calculate myelin maps using the ratio of T1w and T2w MRI images.
>> I saw that the correction of partial volume effects can be used to create
>> the maps (Shafee, Buckner & Fischl, 2015)*.
>>
>> Can I use the PVC functions of PetSurfer for this purpose? And in case I
>> can:
>>
>> Should I apply PVC only on T1? Or also in T2?
>>
>> Which T1 should I use? The original T1 or the T1 with corrections (for
>> example, the nu.mgz file that is corrected for variations in intensity)?
>>
>> Any other advice for calculating myelin maps would be welcome.
>>
>> Thank you in advance,
>>
>> Marina
>>
>>
>> *Link:
>> https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ5T86whDDL8Q-4ZOYG7rMgwoBYIyC4d5BsThH9nR2UT-_82NU3WKyCZrii6txF4QxCWh-K6Hy6aC2vsOwRupJhTnA_Menjtq1hXOSwjndsWxN3BBnw625eBs0OgB8t1ZM0uY7sLR_VuAuMcsvNsQQ9qofNHMaLp6aidYJh3yhta2kwGeWzCXmtyE1XOS-Z2uiDZa5gqmp9A0egHtAOC68aEN1v8l0S-ikEhif20Qg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 9
>> Date: Fri, 28 May 2021 15:11:18 +0000
>> From: "Glasser, Matthew" <glasserm@wustl.edu>
>> Subject: Re: [Freesurfer] PVC to calculate myelin maps
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <61C6E7FB-CD53-4B2C-8487-F9F1BA018FF3@wustl.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> External Email - Use Caution
>>
>> The specific volume to surface mapping we do in the HCP Pipelines minimizes the partial volume effects.
>>
>> Matt.
>>
>> From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Marina Fern?ndez <marina.fdez.alvarez@gmail.com>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Friday, May 28, 2021 at 10:06 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Subject: [Freesurfer] PVC to calculate myelin maps
>>
>>
>>
>> External Email - Use Caution
>> Hi Matt,
>>
>> Thank you very much for the quick answer.
>>
>> We have our data analyzed with another pipeline that also uses Freesurfer functions. For this reason we prefer to calculate myelin maps outside of the HCP Pipelines.
>>
>> Do you think the way of calculating the maps that I explained in the previous question is evenly valid?
>>
>> Best wishes,
>> Marina
>>
>>
>>
>>
>>
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>>
>>
>> Glasser, Matthew<https://secure-web.cisco.com/1EkIb4RUBbvp4aaCzTKvZqXi5mpWtbK6dEiwb2GFTBe5yhOUyifO_hV_E7W1QbzRQK0FwD5cE3KcRI74D3Ovox656ePedxamjtVAEW4AgL4A-7CpFTGP6z5Tq41NoOZ1ojD9zFUJk5ThErtAOajuSKZWvKvti9tqMIHF1q6hCwGlKHevaGmbXlNhh9Qy7R3bO5NIgNuF-fVDEzMvEnu0zjfgN_OsOBclQQKnAUOgbQN0YXzNIZrmOblbk3L2t_TpeCz4wAM71ypty2rwIPsMJYA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Glasser%252C%2BMatthew%2522> Fri, 28 May 2021 07:34:15 -0700<https://secure-web.cisco.com/1ljnBFwkQWFVBlnoXgh6utmDhvf7eskDl5mAoznGoGHO9FTeVRUYQtO-bfot3HqDYDehtfxbJhabnlcLwYGpH0dXP12Y55bVR65aMaKLBI2m5e3DpuIaGvkf3ceK3XJu0-ejvTaS0490ojIjr2iIxgGPOUX8HzFmINOe0OqACHWQa_U11JZn92WpectdOwu7kUNnLEJ1EEOKgypAFQnxBzkuHv-Esidv8bS9Fwbh--pHmipQ4dKxzOK4XeRnn2fte3bTthJQyxPdc-hxBj4-oqg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210528>
>>
>> External Email - Use Caution
>>
>>
>>
>> I would use the HCP Pipelines for this.
>>
>> Matt.
>>
>>
>>
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> Marina Fern?ndez<https://secure-web.cisco.com/1jnEmX8pyslFDNAKq1ESVKhaVYgavR5DWrZDCQVw6EIjIeRPu8VsMW2BmjjGD5q-TEhUnOvxdrLSTT5-Y6k0YXgDL7svI9z3nYXjvFbLZ7RTupBSGPm81_9ITZGgKJJOgPJdln72nUn8_i_M0BwX5vAQJhvU59P4tJ425dDyWnDLjXoT8Isqf8qqqez-ioXBS40q0Uny8MDDL0kBndUynxMfDLd8eLFxK2zhH_m6k3AE0fJN7n9AYbodo3QU0dDBjU5tlYbAcURsJL_uHxBtJ5Q/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Marina%2BFern%25C3%25A1ndez%2522> Fri, 28 May 2021 07:26:19 -0700<https://secure-web.cisco.com/1ljnBFwkQWFVBlnoXgh6utmDhvf7eskDl5mAoznGoGHO9FTeVRUYQtO-bfot3HqDYDehtfxbJhabnlcLwYGpH0dXP12Y55bVR65aMaKLBI2m5e3DpuIaGvkf3ceK3XJu0-ejvTaS0490ojIjr2iIxgGPOUX8HzFmINOe0OqACHWQa_U11JZn92WpectdOwu7kUNnLEJ1EEOKgypAFQnxBzkuHv-Esidv8bS9Fwbh--pHmipQ4dKxzOK4XeRnn2fte3bTthJQyxPdc-hxBj4-oqg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210528>
>>
>> External Email - Use Caution
>>
>>
>>
>> Dear experts,
>>
>> I want to calculate myelin maps using the ratio of T1w and T2w MRI images.
>>
>> I saw that the correction of partial volume effects can be used to create
>>
>> the maps (Shafee, Buckner & Fischl, 2015)*.
>>
>>
>>
>> Can I use the PVC functions of PetSurfer for this purpose? And in case I
>>
>> can:
>>
>>
>>
>> Should I apply PVC only on T1? Or also in T2?
>>
>>
>>
>> Which T1 should I use? The original T1 or the T1 with corrections (for
>>
>> example, the nu.mgz file that is corrected for variations in intensity)?
>>
>>
>>
>> Any other advice for calculating myelin maps would be welcome.
>>
>>
>>
>> Thank you in advance,
>>
>>
>>
>> Marina
>>
>>
>>
>>
>>
>> *Link:
>>
>>
>>
>> https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ5T86whDDL8Q-4ZOYG7rMgwoBYIyC4d5BsThH9nR2UT-_82NU3WKyCZrii6txF4QxCWh-K6Hy6aC2vsOwRupJhTnA_Menjtq1hXOSwjndsWxN3BBnw625eBs0OgB8t1ZM0uY7sLR_VuAuMcsvNsQQ9qofNHMaLp6aidYJh3yhta2kwGeWzCXmtyE1XOS-Z2uiDZa5gqmp9A0egHtAOC68aEN1v8l0S-ikEhif20Qg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48
>>
>>
>>
>>
>>
>>
>>
>> ________________________________
>> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
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>>
>> ------------------------------
>>
>> Message: 10
>> Date: Fri, 28 May 2021 16:16:47 +0100
>> From: Francisca Ferreira <francisca.aff@gmail.com>
>> Subject: [Freesurfer] (no subject)
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>> <CAHj3193cz0dsh9NbkdV1emtHH0YECUZhhWnegm5ySGFr15DxBg@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> External Email - Use Caution
>>
>> Dear Experts,
>>
>> I have extracted subcortical vols corrected for intracranial vols using
>> asegstats2table and I ran mri_glmfit using the following command
>>
>> mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C
>> groupdiff.mtx \--glmdir aseg.glmdir
>>
>> this seems to have worked.
>> I am now trying to visualise my results adapting the recommended wiki
>> command
>>
>> freeview -f
>> /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5
>> -viewport 3d
>>
>> Freeview crashes and I'm getting the following error
>>
>> Number of vertices in overlay data (64 or 64) does not match with surface
>> (163842).
>> Number of vertices in overlay data (64 or 64) does not match with surface
>> (163842).
>>
>> Is there something wrong with the commands priot to this step?
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/19MxmZ-YngtXyjI8JhMif3nT9Tvss_ZmhVPTJcv7XmEmCXzu8Jy5NKIpxAAHF_M_PNz7_3o3mwUbHDADwFceLVaYl52OiJkQSu0DbKoztNgPIvgr8iPRINDSGGxfhgDXGnxZKAN9yo2NojcESoYkDDWlD8UPx0ST1HsPUowbRmRGXkPbhBAURA22d_OZqGj_UEZ-h5ZsaUL5wwI77BYUH5d_kgqMGNdhlshXSOWY6Gyd0hjEbTt_vjFR9UW0PZDouDByVW-FULZfN4r8U_gXjAA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>
>> End of Freesurfer Digest, Vol 207, Issue 54
>> *******************************************
>
> _______________________________________________
> Freesurfer mailing list
> 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/freesurfer
------------------------------
Message: 2
Date: Fri, 28 May 2021 15:35:50 -0400
From: Daniel Davidson Callow <dcallow@umd.edu>
Subject: Re: [Freesurfer] Hippocampal Subfield error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAFMVdsfv5kEkptnvrCPORWwjPPM+2XCpPCZL4vSK_7fDYeZFGw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Sure, what is the best way to share it with you? and which folders/files
should I send?
On Fri, May 28, 2021 at 3:28 PM Iglesias Gonzalez, Juan E. <
JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
> It seems the linear registration is dying. Would you mind sharing the
> subject, please?
> Cheers,
> /E
> Juan Eugenio Iglesias
> Senior research fellow
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
> http://secure-web.cisco.com/1gT1t332MrjlumWoLsCvCODpcjL_Q7MljRoRdHSVXsW_jLPgjmaoLw7W3F0bWnNAuU_i6YcvUn1CduipTCLoLmI28KrJsxObJ-pJjn0aT42elUDeQDY-VOqdDAsm_XCSLk6O0cQQsHQZ_WeLdLkkSP0ZqAF22pxtjRYWOS_mGB4DgjcwDWt2LSx_Vl4dfFH7q6x0dS6wAUxGejm01T0GyOn03KUjtR1Y7XZ1AVi0U9kSfev4sOmBR8c1iZDmEC4jy_1ZRJ6fDyEI8ZlK8tFektA/http%3A%2F%2Fwww.jeiglesias.com
>
> On May 28, 2021, at 12:20, Daniel Davidson Callow <dcallow@umd.edu> wrote:
>
> External Email - Use Caution
>
> Hello Juan,
>
> I am using data from the HCP aging dataset which has a T1 and a
> high-resolution hippocampal scan (T2).
>
> Yes, it does seem that the T2 and T1's are roughly aligned to each other.
> It seems like it has something to do with the creation of the
> tmp/hippoSF_T1T2_v21_highres_left/ folder where the program is expecting
> something to be produced that is not there/hasn't been produced.
>
> Again, here is an example of the code output/error.
>
> @ linenum = 1
> cd /data/bswift-1/dcallow/aging/freesurfer
> set subj= ( HCA8587705_V1_MR )
> rm: No match.
> rm -rf
> /a/ha-nfs-2-ib/export/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/IsRunning.lh+rh
> cd /data/bswift-1/dcallow/aging/freesurfer
> echo HCA8587705_V1_MR
> HCA8587705_V1_MR
> segmentHA_T2.sh HCA8587705_V1_MR
> /data/bswift-1/dcallow/aging/imaging/HCA8587705_V1_MR/unprocessed/TSE_HiResHp/HCA8587705_V1_MR_TSE_HiResHp.nii.gz
> highres 1
> #--------------------------------------------
> #@# Hippocampal Subfields processing (T1+T2) left Fri May 28 12:05:35 EDT
> 2021
> ------------------------------------------
> Setting up environment variables
> ---
> INFO: error loading libraries in default configuration, trying with MCR
> libraries only
> LD_LIBRARY_PATH is
> .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswif$Registering
> norm.mgz to additional volume
> No more processes.
> ERROR: could not open
> /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh
> for reading
> ERROR: loading
> /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh
> as MGH
> Warning: File
> '/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh'
> not found.
> [^H> In myMRIread at 64
> In segmentSubjectT1T2_autoEstimateAlveusML at 186]^H
> Attempt to reference field of non-structure array.
>
> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 188)
> MATLAB:nonStrucReference
> @#@FSTIME 2021:05:28:12:05:35
> run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 7.49 S 0.61 U 6.79 P
> 98% M 283156 F 0 R 84320 W 0 c 2392 w 9596 I 0 O 85080 L 5$@#@FSLOADPOST
> 2021:05:28:12:05:42 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
> 60.45 53.15 38.08
> Linux compute-4-33.bswift.umd.edu
> <http://secure-web.cisco.com/1sqdwOUu2B9k20N1ZAF2G3AjMOwj2lJePh4GNFQiYhImRJsLReMbcU3SXEBp36HD81jqxGdU8a11rJylMhtgbY4fajAEU2pMYsr0DVpWBlkaOMa76fsceUrIl9aQQGsiXc4t6jAY6yGgeO2kzpjftDgTb1eWEbDGuGccb2HunIGkKRrj0yIIhMCUBXNMsPGxCpYhRthsOcBxVagqqmQZxB5PmjkPPc4BKyyMN_eLiZEjt4ui6aNQG76WiX_3leabsXT0Dc4AQ7eKoT8OWNqqHcQ/http%3A%2F%2Fcompute-4-33.bswift.umd.edu>
> 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64
> x86_64 x86_64 GNU/Linux
>
> T2 hippocampal subfields exited with ERRORS at Fri May 28 12:05:42 EDT 2021
>
> For more details, see the log file
> /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/hippocampal-subfields-T2.highres.log
>
>
> Any ideas what might be causing this error. Again, it seems to be working
> for a small subset of participants however, the majority are failing with
> this error.
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> dcallow@umd.edu <dcallow@gmail.com>
> 443-254-6298
>
>
>
> On Fri, May 28, 2021 at 9:32 AM Iglesias Gonzalez, Juan E. <
> JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
>
> Dear Daniel,
>>
>> Are the T2s and T1s roughly aligned in RAS (physical coordinates)? In
>> other words: do they (roughly) overlap when you open them together in
>> Freeview?
>>
>> 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/1gT1t332MrjlumWoLsCvCODpcjL_Q7MljRoRdHSVXsW_jLPgjmaoLw7W3F0bWnNAuU_i6YcvUn1CduipTCLoLmI28KrJsxObJ-pJjn0aT42elUDeQDY-VOqdDAsm_XCSLk6O0cQQsHQZ_WeLdLkkSP0ZqAF22pxtjRYWOS_mGB4DgjcwDWt2LSx_Vl4dfFH7q6x0dS6wAUxGejm01T0GyOn03KUjtR1Y7XZ1AVi0U9kSfev4sOmBR8c1iZDmEC4jy_1ZRJ6fDyEI8ZlK8tFektA/http%3A%2F%2Fwww.jeiglesias.com
>> <http://secure-web.cisco.com/1M43tYnBIwe0As03lwnAGcBzSZfvIXhP_UsjatHKyZUaaQ4wSAHDh_rwH1615JlqcHfPYywTwRzVbI_to9hVZq--leXJy2p4Zrh_mUI3lNII4SXa870Dh3HPFfDvztZQqR8Lzb5jZgrooucfAyVmWEBNMCuB8-mMhkfQpliBwpQ4AlrLgpwXKROaATxslozZ45t7me-SsaBv2pGfPGHhefMDQiyWYTTwRkiWX5UsaBqKv7GznpWuae2cijb7yGp0Ot534fYLsrPfsPuzrmK7NMQ/http%3A%2F%2Fwww.jeiglesias.com>
>>
>>
>> On May 28, 2021, at 07:53, Daniel Davidson Callow <dcallow@umd.edu>
>> wrote:
>>
>> External Email - Use Caution
>>
>> Hello,
>>
>> I am running into errors when running
>>
>> segmentHA_T2.sh ${subj}
>> /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
>>
>> Approximately 10% of my subjects are being processed but for some reason,
>> the majority fail to execute. Here is an output from the error log.
>> ------------------------------
>> USER dcallow
>> HOST compute-4-32.bswift.umd.edu
>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
>> PROCESSID 4033
>> PROCESSOR x86_64
>> OS Linux
>> Linux compute-4-32.bswift.umd.edu
>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu> 2.6.32-754.35.1.el6.x86_64
>> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>> ------------------------------
>>
>> #--------------------------------------------
>> #@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT
>> 2021
>> ------------------------------------------
>> Setting up environment variables
>> ---
>> INFO: error loading libraries in default configuration, trying with MCR
>> libraries only
>> LD_LIBRARY_PATH is
>> .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering
>> norm.mgz to additional volume
>> makeIsotropic WARNING: not different enough, won't reslice!
>> No more processes.
>> ERROR: could not open
>> /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
>> for reading
>> ERROR: loading
>> /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
>> as MGH
>> Warning: File
>> '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh'
>> not found.
>> [^H> In myMRIread at 64
>> In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H
>> Attempt to reference field of non-structure array.
>>
>> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211)
>>
>>
>>
>> MATLAB:nonStrucReference
>> @#@FSTIME 2021:05:27:21:39:51
>> run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61
>> P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST
>> 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
>> 31.22 29.74 28.95
>> Linux compute-4-32.bswift.umd.edu
>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu> 2.6.32-754.35.1.el6.x86_64
>> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>>
>> T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT
>> 2021
>>
>> I am also getting a matlab_crash_dump file
>>
>> ------------------------------------------------------------------------
>> Segmentation violation detected at Thu May 27 21:51:52 2021
>> ------------------------------------------------------------------------
>>
>> Configuration:
>> Crash Decoding : Disabled
>> Current Visual : None
>> Default Encoding : US-ASCII
>> GNU C Library : 2.12 stable
>> MATLAB Architecture: glnxa64
>> MATLAB Root : /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux
>> <http://secure-web.cisco.com/1zf_ot3cQGUvMhTgphfJ7towMivhNxWKqA3AayyU_OPHHiMasb-EvBGTFN3sYYJDfq2OTyGKzBZ_szFAJCXZHlZGEtJjl-Jdhb4Q1bIAonDtiewkPoyMXUpsAcQaKfsBE0RsmUc-YGdemu96LMj476x2UIb3GfDNjDVx7ULnA6ydsfS5RHTfxedRiKFt6oLIZ-8AmzrNc44dziwIEz2Tm1zVXkZba_ISfg8fwql2KxoL8WGjCE7_3XIDrEbE-HNmMPhnNu3asRalw0_AJ6BOTkA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux>
>> MATLAB Version : 8.4.0.150421 (R2014b)
>> Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29
>> 04:45:43 EDT 2020 x86_64
>> Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
>> Software OpenGL : 0
>> Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java
>> HotSpot(TM) 64-Bit Server VM mixed mode
>> Window System : No active display
>>
>> Fault Count: 1
>>
>>
>> Abnormal termination:
>> Segmentation violation
>>
>> Stack Trace (from fault):
>> [ 0] 0x00007f2b30f06213
>> /lib64/libpthread.so.0+00033299 pthread_join+00000035
>> [ 1] 0x00007f2a9f4d847d
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 2] 0x00007f2a9f4d8cac
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 3] 0x00007f2a9f5cae63
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 4] 0x00007f2a9f5af896
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 5] 0x00007f2a9f5a6b8d
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 6] 0x00007f2a9f5a6fd0
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 7] 0x00007f2a9f5aad00
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 8] 0x00007f2a9f5a5c3c
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 9] 0x00007f2a9f44fb03
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 10] 0x00007f2a9f42b9cc
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 11] 0x00007f2a9f42b132
>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>> 12] 0x00007f2b21dcfc0a /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538
>> <http://secure-web.cisco.com/15wmunFtJy8RzDq9oVQoOhvMj4SqFWIMICnRxUk7kN3uyYtej40W1KAf2FgN8p-YHhCe94AM96CLuzs2_pg0h5a-wPhOcAbQDBbn9UroNugqM9zMNW_x85lUFfPpgR5eVTK_sVWwcg4CiDnJkgZm34QYRBZBTcAYN9riNJ9m1rpj4PKAxhbRXEmUfM_1qcroQ-tCUoHaYthJ1wh2oe_rXJu65oN57rZkO5uN2D-kO6NX50rAL6N-yYqFbQTvlWSoqZXcpaDvh0nH11oRbZSCgYQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmex.so%2B00150538>
>> mexRunMexFile+00000090
>> [ 13] 0x00007f2b21dcc5c4 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00136644
>> <http://secure-web.cisco.com/1VNIP2TP7g_-k-V3EXmoqH3gSLCQPAVKDrJmmFHk4DSCIs8dpaPhlMZY3o1R2Gcl45b59huNzCHAuDXy3Jk_DTzSHWeoAdTGEyyL_kxblZnIJkrmRuC21lPT3uRUUA5F-hhCNI4L1ewaawelx52Ns4n9o9ra_oWhRf9AD84pTyjJnXGVX1FrlCKhr8xCI3BxucHGenwthYaUBlmin56HnLgin-otSEMgaMDZVIlfwdsJjpm_sB9ATY4IgK9GI4jaKI7g9MMLbHjEVqHgacPW6sw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmex.so%2B00136644>
>> [ 14] 0x00007f2b21dcd414 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00140308
>> <http://secure-web.cisco.com/1DHyyF-k0XGkPk9gRiFdvyrzyhAwZmrJ8Vpas5l1bhBSmDpXf1DE5cQ_3mHR9xgFvggvUyK6nS-KPKUap_Y3PtkQxvO-b174nhgWgkAkhqF0GCz9M2ffTgT-YPppDR2yc8dr-rFkMth1BYS8tXsV0l1UcZ8aP_QkA_xu_XEQ-IULq2naXsfdbIOmnONEUC_6gpFEpp2_EkJr0prYDw63-Fcx2DNkGKP9H_lYz9w8au_3bwu-8Upbm2dSza-8ykxGxxKbsp1J3VugjWqfirkKTxg/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmex.so%2B00140308>
>> [ 15] 0x00007f2b232ff329 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>> <http://secure-web.cisco.com/1YvAiBC_3G9VAawE4steKXeCaNTlrpgMnQG_qhwLeycblS635IsShf_UEZVAtvWU98ic7nFoyTObuenzWyfIOrdZ1ukAI2_Rwpr7BFODPD8xr8FVnAIglj8lndurD-18acdOLCAx9cl__2Xe2_21LZQn4auLKXubsYP6cvn7ODCEtX6tup_3H0vUFEZ4WQGRknJISa7pBZBc8A0cMb8ooCFDVafzDFjkSj4EiKd-9hl01YeUQPAu5Hwt6s7FUSKNmxksu_SyBfaeCpYE8OvqpHA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_dispatcher.so%2B00791337> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[
>> 16] 0x00007f2b2260fb70 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
>> <http://secure-web.cisco.com/1FqlnK1mbYe0fc4WrLh27McIgFcpF4caZpprfvWHGIiLLoxXo6_L3M8BINfHY5-jSh1ngRLTREAlaV-ecKWLXgaZmAvPaE1WcZ3K8NB0Vvxh-3_asNJndl8j3D5yqTCWCZygCAlsQE2BScTJzzzgOg0nDdICKmBjoe5NmIpTDU8e12QBMlVY4gLY59bk2WU5NEVeEhnmukrN_bzXIchegVXLsx6fumnKQzIoSHTfUwa7LAM4D8pzDWBH7hsRyezlzADNhYYUpmOqNOqn5JFOEDA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04053872>
>> [ 17] 0x00007f2b225bfe02 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
>> <http://secure-web.cisco.com/1oFCMQbMq8_LNNSwavId3uL9KorlKBV-Dq9AH2k9--Ptuwe56v1f0M8oNm9UBgRvAQacl9RKg1Qg0DY7ko-IcvfQe-2sfN0qRBoXdPr8AINOFM5HQFjasYlRzdVlc-G_JqKNPbJEzsVRjfXLn9CA4BIE2htjH6A3_wsQTimZoAzJF_HNTmhJ7qA5E1fFaDN7kOubeJKvBSvnuTwu-bMBUREZA03ALLxwcXdU7Zf9awXp32KrUJr3sssPhgqjOZm0-uLmk2eWzYlnYg6SD7XCpag/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03726850>
>> [ 18] 0x00007f2b225c2022 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
>> <http://secure-web.cisco.com/1mkHocgN-E2JcT6SI0pNs-oXMVy5k5oGB6gATPm9NI82pijbaPsiS_mVu6yD_8ldltWLoJH4dyPp4vYVPvfXnMD03lmxENx9NH-5f5d00CK147UzH945ZVfrdnKRmxtQZPQAbtHNrwjMC7s4lNIqHSR7GSaetK6V29YMKzu_-Tu1SwwBDg3JePYZjvodQRdYUkHEfs8YmahPAtNRQPM3MskmCOUcjL4tV6sdY1yfjwhrpmPrjlQKVXgKZQMDqosdS_VLmyb6B_maYrhrDgnW0aA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03735586>
>> [ 19] 0x00007f2b225c7f87 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
>> <http://secure-web.cisco.com/1IXEh5f9oNhkKzllddjiYB3PrZZ0_a0EZYlGzFTPY7IyKerNHNEwXaFMOYZXMm4hct0Rom3hL_ou_TGy8UJSc7P-OrfKK0CrXSeDSR-7YEwoHUr9hq-a_cceHo-B4JS3oLxWaU0ykCPBleBOrFVoTgQHmHnKJTjxDY5GAIqCi48jEIy7iuEXH8AMIgvxL5dbjDgjN_qtXvhWG70-bIbaIS0j25znSUF0ho6j9W7Q-okSGwCZJ0YkWBJerVuCH5b3o_Rr2u-KSeDxXNKED0dtlBw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03760007>
>> [ 20] 0x00007f2b225c36ff /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
>> <http://secure-web.cisco.com/1z7kRHrPDXQ2J89IxYNotG6f3AWl-VlFzlspUBbkrsL1gDgJbVg7Jvui01VXzy_9XgOLBM7uiNrNy2emqwnaZRVr97UmD81gSG0_F-eUpsqBkSrR3o5bOkcSlKSKbnIJLwrb7IlUi1lGu-eqqDsDfvtd8bmEZ9LWhsNqU63v-ByjHg8-Tppp8IHXCegbHJwtiYG5b7ldmmACZL3zXlOMT5m_Xf7vUxnL9hQ9AOVduNe9rwSJml83zaACIYRO7148iHaaWASzcChMIFktUQdn6DA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03741439>
>> [ 21] 0x00007f2b225c4334 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
>> <http://secure-web.cisco.com/1Qidv5KKgCpV0A4yNcjeOaCG5BbPEneNCG_VGPSEeihppLC0K8VCKQKqgycrF_JG7hDWxESiIkJ0zZSKIoEcr9MBBq-zCjGrXAT3o-uxNgPfkPx2Diq5rB4I4Nj_5SOHSz67iis8FUiswPfla7T1ax5dsZbZqWNZzf3mRlN9H7qfLp7x9gNQlbo1DsK8hFvHTUGz_PM_4onSpO9CffOK0BfVEfeOpXOHy6EjznUeUWhuJyx6dorWoftGwaDXEKw44ZGcYPHdtnJXKpRfHp8TKpw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03744564>
>> [ 22] 0x00007f2b2263952e /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
>> <http://secure-web.cisco.com/1LFwdsCWta1IKYv3k3YydtSX7z6ZkdwRsguf-SFigI8Kxt4X2FK9QjJHavPcu2kTMH1M8_iHldk2sCDW-6Cw6fokp46WGvsOCfyh25z_jqednT1Bw_Rij1zigZ9QCabcdCHHrRmXYLySPYEVnuaTn22efOadhUo6Nk4TlR0yJ9IkLdzQFrQh_3bCoEoX8T_dZVAmOpLbfqeCTnXHh06TvfZx3I9xWFZvsuURivUTNG_DPyZpHm1y05pMXl4mY_b6ff5sdtFbOIGeh7kop0ZDDEw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04224302>
>> [ 23] 0x00007f2b232ff329 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>> <http://secure-web.cisco.com/1YvAiBC_3G9VAawE4steKXeCaNTlrpgMnQG_qhwLeycblS635IsShf_UEZVAtvWU98ic7nFoyTObuenzWyfIOrdZ1ukAI2_Rwpr7BFODPD8xr8FVnAIglj8lndurD-18acdOLCAx9cl__2Xe2_21LZQn4auLKXubsYP6cvn7ODCEtX6tup_3H0vUFEZ4WQGRknJISa7pBZBc8A0cMb8ooCFDVafzDFjkSj4EiKd-9hl01YeUQPAu5Hwt6s7FUSKNmxksu_SyBfaeCpYE8OvqpHA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_dispatcher.so%2B00791337> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[
>> 24] 0x00007f2b2260fb70 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
>> <http://secure-web.cisco.com/1FqlnK1mbYe0fc4WrLh27McIgFcpF4caZpprfvWHGIiLLoxXo6_L3M8BINfHY5-jSh1ngRLTREAlaV-ecKWLXgaZmAvPaE1WcZ3K8NB0Vvxh-3_asNJndl8j3D5yqTCWCZygCAlsQE2BScTJzzzgOg0nDdICKmBjoe5NmIpTDU8e12QBMlVY4gLY59bk2WU5NEVeEhnmukrN_bzXIchegVXLsx6fumnKQzIoSHTfUwa7LAM4D8pzDWBH7hsRyezlzADNhYYUpmOqNOqn5JFOEDA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04053872>
>> [ 25] 0x00007f2b225bfe02 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
>> <http://secure-web.cisco.com/1oFCMQbMq8_LNNSwavId3uL9KorlKBV-Dq9AH2k9--Ptuwe56v1f0M8oNm9UBgRvAQacl9RKg1Qg0DY7ko-IcvfQe-2sfN0qRBoXdPr8AINOFM5HQFjasYlRzdVlc-G_JqKNPbJEzsVRjfXLn9CA4BIE2htjH6A3_wsQTimZoAzJF_HNTmhJ7qA5E1fFaDN7kOubeJKvBSvnuTwu-bMBUREZA03ALLxwcXdU7Zf9awXp32KrUJr3sssPhgqjOZm0-uLmk2eWzYlnYg6SD7XCpag/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03726850>
>> [ 26] 0x00007f2b225c2022 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
>> <http://secure-web.cisco.com/1mkHocgN-E2JcT6SI0pNs-oXMVy5k5oGB6gATPm9NI82pijbaPsiS_mVu6yD_8ldltWLoJH4dyPp4vYVPvfXnMD03lmxENx9NH-5f5d00CK147UzH945ZVfrdnKRmxtQZPQAbtHNrwjMC7s4lNIqHSR7GSaetK6V29YMKzu_-Tu1SwwBDg3JePYZjvodQRdYUkHEfs8YmahPAtNRQPM3MskmCOUcjL4tV6sdY1yfjwhrpmPrjlQKVXgKZQMDqosdS_VLmyb6B_maYrhrDgnW0aA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03735586>
>> [ 27] 0x00007f2b225c7f87 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
>> <http://secure-web.cisco.com/1IXEh5f9oNhkKzllddjiYB3PrZZ0_a0EZYlGzFTPY7IyKerNHNEwXaFMOYZXMm4hct0Rom3hL_ou_TGy8UJSc7P-OrfKK0CrXSeDSR-7YEwoHUr9hq-a_cceHo-B4JS3oLxWaU0ykCPBleBOrFVoTgQHmHnKJTjxDY5GAIqCi48jEIy7iuEXH8AMIgvxL5dbjDgjN_qtXvhWG70-bIbaIS0j25znSUF0ho6j9W7Q-okSGwCZJ0YkWBJerVuCH5b3o_Rr2u-KSeDxXNKED0dtlBw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03760007>
>> [ 28] 0x00007f2b225c36ff /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
>> <http://secure-web.cisco.com/1z7kRHrPDXQ2J89IxYNotG6f3AWl-VlFzlspUBbkrsL1gDgJbVg7Jvui01VXzy_9XgOLBM7uiNrNy2emqwnaZRVr97UmD81gSG0_F-eUpsqBkSrR3o5bOkcSlKSKbnIJLwrb7IlUi1lGu-eqqDsDfvtd8bmEZ9LWhsNqU63v-ByjHg8-Tppp8IHXCegbHJwtiYG5b7ldmmACZL3zXlOMT5m_Xf7vUxnL9hQ9AOVduNe9rwSJml83zaACIYRO7148iHaaWASzcChMIFktUQdn6DA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03741439>
>> [ 29] 0x00007f2b225c4334 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
>> <http://secure-web.cisco.com/1Qidv5KKgCpV0A4yNcjeOaCG5BbPEneNCG_VGPSEeihppLC0K8VCKQKqgycrF_JG7hDWxESiIkJ0zZSKIoEcr9MBBq-zCjGrXAT3o-uxNgPfkPx2Diq5rB4I4Nj_5SOHSz67iis8FUiswPfla7T1ax5dsZbZqWNZzf3mRlN9H7qfLp7x9gNQlbo1DsK8hFvHTUGz_PM_4onSpO9CffOK0BfVEfeOpXOHy6EjznUeUWhuJyx6dorWoftGwaDXEKw44ZGcYPHdtnJXKpRfHp8TKpw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03744564>
>> [ 30] 0x00007f2b2263952e /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
>> <http://secure-web.cisco.com/1LFwdsCWta1IKYv3k3YydtSX7z6ZkdwRsguf-SFigI8Kxt4X2FK9QjJHavPcu2kTMH1M8_iHldk2sCDW-6Cw6fokp46WGvsOCfyh25z_jqednT1Bw_Rij1zigZ9QCabcdCHHrRmXYLySPYEVnuaTn22efOadhUo6Nk4TlR0yJ9IkLdzQFrQh_3bCoEoX8T_dZVAmOpLbfqeCTnXHh06TvfZx3I9xWFZvsuURivUTNG_DPyZpHm1y05pMXl4mY_b6ff5sdtFbOIGeh7kop0ZDDEw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04224302>
>> [ 31] 0x00007f2b232ff329 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>> <http://secure-web.cisco.com/1YvAiBC_3G9VAawE4steKXeCaNTlrpgMnQG_qhwLeycblS635IsShf_UEZVAtvWU98ic7nFoyTObuenzWyfIOrdZ1ukAI2_Rwpr7BFODPD8xr8FVnAIglj8lndurD-18acdOLCAx9cl__2Xe2_21LZQn4auLKXubsYP6cvn7ODCEtX6tup_3H0vUFEZ4WQGRknJISa7pBZBc8A0cMb8ooCFDVafzDFjkSj4EiKd-9hl01YeUQPAu5Hwt6s7FUSKNmxksu_SyBfaeCpYE8OvqpHA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_dispatcher.so%2B00791337> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[
>> 32] 0x00007f2b225ecbf0 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03910640
>> <http://secure-web.cisco.com/1XY2HS1eoFmCZj_0FLnEggB0qkNY41bJhNhIxrQkYQlfUUFOeH7A1s1kvm8DQWM0JlgCJOvl0vJiumfWqWZpNqcPopcWLIVMrGP89FTG4LxSpueiRrp0XpSeQ-vDq_Gp62up2g5nwwIVcmd7-oGNZmWQzFkkViXG0-KZbB3pU0t5L9QDBRtqK8nLjqVkLlKjqncDvdWTxmejTP9mpEj20zQuBbn_-88xbgdpbszqvtvKEThIjeHxG57d1SeK3JuQLoJ9FFtxjVfLmaIa15EmzgQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03910640>
>> [ 33] 0x00007f2b225ec449 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03908681
>> <http://secure-web.cisco.com/15RN_eXEIUAO_WqqYNIIAMljnNJvT34HmTcfAnwdPgjQ5Zs_ljlxOt3x13LTRvM7d5IunUlOUz5aKZ7GubCOSwKdOyfM_N8vvu2s8rcvMi_VSMoOHrf9PjqE-VmSGbzKW0i_9a6AXA6ZDjAeKelV7RTipDEECT6fzvwMMYPf94nguZ7fEEF4bMoM2nZHkvhvuZGI_ZTO8PGtiq5ntFL907fj7pH9SWOuz8Nk9t5X7rPPQ0ntQShuBYa89QKVU2cfmhQRoAogbmYs22gLetkR8ZQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03908681>
>> [ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03137494
>> <http://secure-web.cisco.com/1XibXIDoYPELJ8Qmp8ylDzLuf8aUubO7-jyooiQCEf8a082UlM2DJiqW5LaFdKT1yQJbxTKlXm1N_dBVMT-orB0SEIbRxWaLJDGWLozzZ8D-UhNRaYXYgWHAzjvA6draUI0HwfhbOmcDglBW0Q06X4mOA2cCvheWHU-rDg5mA3PdplDBSiG6JmbgZg-feiB947xEiq2BUD8ZrJe9j8XTPhjYBed6n1I_4WbG9tNT1YNCCpzNtFjBtVwnO-NTCN4QbXB2UmoKnv8og7_XILbQrEg/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03137494>
>> inCallFcnWithTrap+00000086
>> [ 35] 0x00007f2b225b3c0b /export/rel60_shadow/
>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03677195
>> <http://secure-web.cisco.com/1IAIH2i6-h19TW-GQXcC6sE7doC05sQYZagDqPgNU7ylypApwktFIOYKOoaKDLZKVt6j1FAmWztWJ2TpLtqqgQ_JPtZUaeDVOLW6CQR7hI9SuV0fizRPOBwBdGUHvBvKq2W35Tmj27nCuylilBfvIx_fAJmYZvwD8WFgDdLEl4sZmL812gt0QLdUyaJa5Av3bXoLMpCjFcB1nM8CY9SVYRn98cmJyTHQ5hRsVF0m8j3uzDgGf6cW5wRbtzDfQ2RQG8zgWtA8CAoUH_oMeziILfA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03677195>
>>
>> This error was detected while a MEX-file was running. If the MEX-file
>> is not an official MathWorks function, please examine its source code
>> for errors. Please consult the External Interfaces Guide for information
>> on debugging MEX-files.
>>
>> If 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://secure-web.cisco.com/1ToP028W189wddEaTLTOlStcqTkqBXXpwQm5XlMzJrck9Hq2kTADtwO5bt2kl-U5pK8qbajPh8WbP6tOgzn8YJLXOiKTq_8JGickLYtn0ui0aXBuNmsvVnr_TQIcwu5ivcQh2Z73jsMT1S7VFz__fVMvnJkrO5FTcOwK2R6WJwc-Qwwoy9ozQYXNWvJQ1d7gCpfRUHaLQgHwD9LGG8d4glUgwuSzU54rdtIKUtOSy0g-DM3rjXsbinbP1Welm-keUcB_MsXLd_aWApVIgcz4Y3w/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
>> <http://secure-web.cisco.com/1B8en4WQVOmBM-TonUpSzamw674QdqjI_ltVT2KdTcbPbuPW0K3Ay8KDhD5c4RCuwKYVmR07FjU0Aevx09ahCMeyv0JkXQ52Hmhwb4sx7s4JboH2NUrlUAj_t1NiR1NWXsdcBbrW2ARL_QZIvDtzEvCZllOY4TGkavTAZNKXychD1QqvsZFE-MKZXZcrP5pagoPPejJGw9gWjGYxJHuPexjzzMvAZ00KWwGungv_lBCKCFbVfyIShsbLN-xOO4h3eWRUjCNBh0HGJu8phyXt6Xg/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F>
>>
>> A technical support engineer might contact you with further information.
>>
>> Any insight or help you can provide is greatly appreciated.
>> *Daniel Callow*
>> *PhD Student, Neuroscience and Cognitive Science*
>> Exercise for Brain Health Lab
>> University of Maryland, College Park
>> dcallow@umd.edu <dcallow@gmail.com>
>> 443-254-6298
>>
>> _______________________________________________
>> 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/1jsYurSjDkGLI1-FXY0m-g6eynNSH2B64GSTOT1rHMjSjL7kIkfgKV2zmlJPeBvA-TEVNAom0uKRZNC6T9sZBy14KcgdYWMVG7kY74X1XiBBJsat99Dd13x0rDvSPQ_ZsHdqjh5k7NEgH53EIs3OyAPn3u1TEOQiO9Jc1HlBv8y_Xv-Fw4rjHlXw5_LtjitzefDiVcas7hloDVAV6zNI93mxW9z-Kp8TebW8Mv_BjZtcCRAvCi0yWr_6yADWQB6IwNjyBDeNCbzrmb8_Q0XVVFQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1A8bx9DXo139MZ9fUyweH53j6yZXrv_4CRKnXmAPk9kBzduToxLkj1vZWvmLonEsFp84m6XFRXlYrhqS8cUoh9IzqRFztAI5adQtTo4Iy_XLJDMVWzFhr8eviVP41cbGOZYMq4fcW46zm8_oSEJfCriPqueW-7MMEvbUq6BQ_zYUYkkXKjDakz6kwHoc8IM-ImrVAC_5g5u6nyFnCsRuLDqZXtJtna2vk0JoJ1JKnG0u-uOddmpFE6_Lq7iVk3qSNH1AezDonJ0zHgMvrnYxrCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>
>>
>> _______________________________________________
>> 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/1jsYurSjDkGLI1-FXY0m-g6eynNSH2B64GSTOT1rHMjSjL7kIkfgKV2zmlJPeBvA-TEVNAom0uKRZNC6T9sZBy14KcgdYWMVG7kY74X1XiBBJsat99Dd13x0rDvSPQ_ZsHdqjh5k7NEgH53EIs3OyAPn3u1TEOQiO9Jc1HlBv8y_Xv-Fw4rjHlXw5_LtjitzefDiVcas7hloDVAV6zNI93mxW9z-Kp8TebW8Mv_BjZtcCRAvCi0yWr_6yADWQB6IwNjyBDeNCbzrmb8_Q0XVVFQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1A8bx9DXo139MZ9fUyweH53j6yZXrv_4CRKnXmAPk9kBzduToxLkj1vZWvmLonEsFp84m6XFRXlYrhqS8cUoh9IzqRFztAI5adQtTo4Iy_XLJDMVWzFhr8eviVP41cbGOZYMq4fcW46zm8_oSEJfCriPqueW-7MMEvbUq6BQ_zYUYkkXKjDakz6kwHoc8IM-ImrVAC_5g5u6nyFnCsRuLDqZXtJtna2vk0JoJ1JKnG0u-uOddmpFE6_Lq7iVk3qSNH1AezDonJ0zHgMvrnYxrCA/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
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--
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcallow@umd.edu <dcallow@gmail.com>
443-254-6298
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------------------------------
Message: 3
Date: Fri, 28 May 2021 20:10:16 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal Subfield error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <687A1CEB-C221-4BFB-95C8-86B1F6D5AA2A@mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
Please compress the whole subject directory and upload it to the ftp
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
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
On May 28, 2021, at 15:35, Daniel Davidson Callow <dcallow@umd.edu<mailto:dcallow@umd.edu>> wrote:
External Email - Use Caution
Sure, what is the best way to share it with you? and which folders/files should I send?
On Fri, May 28, 2021 at 3:28 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu<mailto:JIGLESIASGONZALEZ@mgh.harvard.edu>> wrote:
It seems the linear registration is dying. Would you mind sharing the subject, please?
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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com<http://secure-web.cisco.com/1gT1t332MrjlumWoLsCvCODpcjL_Q7MljRoRdHSVXsW_jLPgjmaoLw7W3F0bWnNAuU_i6YcvUn1CduipTCLoLmI28KrJsxObJ-pJjn0aT42elUDeQDY-VOqdDAsm_XCSLk6O0cQQsHQZ_WeLdLkkSP0ZqAF22pxtjRYWOS_mGB4DgjcwDWt2LSx_Vl4dfFH7q6x0dS6wAUxGejm01T0GyOn03KUjtR1Y7XZ1AVi0U9kSfev4sOmBR8c1iZDmEC4jy_1ZRJ6fDyEI8ZlK8tFektA/http%3A%2F%2Fwww.jeiglesias.com>
On May 28, 2021, at 12:20, Daniel Davidson Callow <dcallow@umd.edu<mailto:dcallow@umd.edu>> wrote:
External Email - Use Caution
Hello Juan,
I am using data from the HCP aging dataset which has a T1 and a high-resolution hippocampal scan (T2).
Yes, it does seem that the T2 and T1's are roughly aligned to each other. It seems like it has something to do with the creation of the tmp/hippoSF_T1T2_v21_highres_left/ folder where the program is expecting something to be produced that is not there/hasn't been produced.
Again, here is an example of the code output/error.
@ linenum = 1
cd /data/bswift-1/dcallow/aging/freesurfer
set subj= ( HCA8587705_V1_MR )
rm: No match.
rm -rf /a/ha-nfs-2-ib/export/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/IsRunning.lh+rh
cd /data/bswift-1/dcallow/aging/freesurfer
echo HCA8587705_V1_MR
HCA8587705_V1_MR
segmentHA_T2.sh HCA8587705_V1_MR /data/bswift-1/dcallow/aging/imaging/HCA8587705_V1_MR/unprocessed/TSE_HiResHp/HCA8587705_V1_MR_TSE_HiResHp.nii.gz highres 1
#--------------------------------------------
#@# Hippocampal Subfields processing (T1+T2) left Fri May 28 12:05:35 EDT 2021
------------------------------------------
Setting up environment variables
---
INFO: error loading libraries in default configuration, trying with MCR libraries only
LD_LIBRARY_PATH is .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswif$Registering norm.mgz to additional volume
No more processes.
ERROR: could not open /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh for reading
ERROR: loading /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh as MGH
Warning: File '/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh' not found.
[^H> In myMRIread at 64
In segmentSubjectT1T2_autoEstimateAlveusML at 186]^H
Attempt to reference field of non-structure array.
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 188)
MATLAB:nonStrucReference
@#@FSTIME 2021:05:28:12:05:35 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 7.49 S 0.61 U 6.79 P 98% M 283156 F 0 R 84320 W 0 c 2392 w 9596 I 0 O 85080 L 5$@#@FSLOADPOST 2021:05:28:12:05:42 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 60.45 53.15 38.08
Linux compute-4-33.bswift.umd.edu<http://secure-web.cisco.com/1sqdwOUu2B9k20N1ZAF2G3AjMOwj2lJePh4GNFQiYhImRJsLReMbcU3SXEBp36HD81jqxGdU8a11rJylMhtgbY4fajAEU2pMYsr0DVpWBlkaOMa76fsceUrIl9aQQGsiXc4t6jAY6yGgeO2kzpjftDgTb1eWEbDGuGccb2HunIGkKRrj0yIIhMCUBXNMsPGxCpYhRthsOcBxVagqqmQZxB5PmjkPPc4BKyyMN_eLiZEjt4ui6aNQG76WiX_3leabsXT0Dc4AQ7eKoT8OWNqqHcQ/http%3A%2F%2Fcompute-4-33.bswift.umd.edu> 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Fri May 28 12:05:42 EDT 2021
For more details, see the log file /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/hippocampal-subfields-T2.highres.log
Any ideas what might be causing this error. Again, it seems to be working for a small subset of participants however, the majority are failing with this error.
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
dcallow@umd.edu<mailto:dcallow@gmail.com>
443-254-6298
On Fri, May 28, 2021 at 9:32 AM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu<mailto:JIGLESIASGONZALEZ@mgh.harvard.edu>> wrote:
Dear Daniel,
Are the T2s and T1s roughly aligned in RAS (physical coordinates)? In other words: do they (roughly) overlap when you open them together in Freeview?
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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com<http://secure-web.cisco.com/1M43tYnBIwe0As03lwnAGcBzSZfvIXhP_UsjatHKyZUaaQ4wSAHDh_rwH1615JlqcHfPYywTwRzVbI_to9hVZq--leXJy2p4Zrh_mUI3lNII4SXa870Dh3HPFfDvztZQqR8Lzb5jZgrooucfAyVmWEBNMCuB8-mMhkfQpliBwpQ4AlrLgpwXKROaATxslozZ45t7me-SsaBv2pGfPGHhefMDQiyWYTTwRkiWX5UsaBqKv7GznpWuae2cijb7yGp0Ot534fYLsrPfsPuzrmK7NMQ/http%3A%2F%2Fwww.jeiglesias.com>
On May 28, 2021, at 07:53, Daniel Davidson Callow <dcallow@umd.edu<mailto:dcallow@umd.edu>> wrote:
External Email - Use Caution
Hello,
I am running into errors when running
segmentHA_T2.sh ${subj} /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
Approximately 10% of my subjects are being processed but for some reason, the majority fail to execute. Here is an output from the error log.
------------------------------
USER dcallow
HOST compute-4-32.bswift.umd.edu<http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
PROCESSID 4033
PROCESSOR x86_64
OS Linux
Linux compute-4-32.bswift.umd.edu<http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu> 2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
------------------------------
#--------------------------------------------
#@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT 2021
------------------------------------------
Setting up environment variables
---
INFO: error loading libraries in default configuration, trying with MCR libraries only
LD_LIBRARY_PATH is .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering norm.mgz to additional volume
makeIsotropic WARNING: not different enough, won't reslice!
No more processes.
ERROR: could not open /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh for reading
ERROR: loading /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh as MGH
Warning: File '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh' not found.
[^H> In myMRIread at 64
In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H
Attempt to reference field of non-structure array.
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211)
MATLAB:nonStrucReference
@#@FSTIME 2021:05:27:21:39:51 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61 P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 31.22 29.74 28.95
Linux compute-4-32.bswift.umd.edu<http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu> 2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT 2021
I am also getting a matlab_crash_dump file
------------------------------------------------------------------------
Segmentation violation detected at Thu May 27 21:51:52 2021
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : None
Default Encoding : US-ASCII
GNU C Library : 2.12 stable
MATLAB Architecture: glnxa64
MATLAB Root : /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux<http://secure-web.cisco.com/1zf_ot3cQGUvMhTgphfJ7towMivhNxWKqA3AayyU_OPHHiMasb-EvBGTFN3sYYJDfq2OTyGKzBZ_szFAJCXZHlZGEtJjl-Jdhb4Q1bIAonDtiewkPoyMXUpsAcQaKfsBE0RsmUc-YGdemu96LMj476x2UIb3GfDNjDVx7ULnA6ydsfS5RHTfxedRiKFt6oLIZ-8AmzrNc44dziwIEz2Tm1zVXkZba_ISfg8fwql2KxoL8WGjCE7_3XIDrEbE-HNmMPhnNu3asRalw0_AJ6BOTkA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux>
MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64
Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
Software OpenGL : 0
Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : No active display
Fault Count: 1
Abnormal termination:
Segmentation violation
Stack Trace (from fault):
[ 0] 0x00007f2b30f06213 /lib64/libpthread.so.0+00033299 pthread_join+00000035
[ 1] 0x00007f2a9f4d847d /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 2] 0x00007f2a9f4d8cac /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 3] 0x00007f2a9f5cae63 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 4] 0x00007f2a9f5af896 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 5] 0x00007f2a9f5a6b8d /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 6] 0x00007f2a9f5a6fd0 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab
.mexa64+0$[ 7] 0x00007f2a9f5aad00 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 8] 0x00007f2a9f5a5c3c /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 9] 0x00007f2a9f44fb03 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 10] 0x00007f2a9f42b9cc /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 11] 0x00007f2a9f42b132 /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ 12] 0x00007f2b21dcfc0a /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538<http://secure-web.cisco.com/1
5wmunFtJy8RzDq9oVQoOhvMj4SqFWIMICnRxUk7kN3uy!
Ytej40W1
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[ 33] 0x00007f2b225ec449 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03908681<http://secure-web.cisco.com/15RN_eXEIUAO_WqqYNIIAMljnNJvT34HmTcfAnwdPgjQ5Zs_ljlxOt3x13LTRvM7d5IunUlOUz5aKZ7GubCOSwKdOyfM_N8vvu2s8rcvMi_VSMoOHrf9PjqE-VmSGbzKW0i_9a6AXA6ZDjAeKelV7RTipDEECT6fzvwMMYPf94nguZ7fEEF4bMoM2nZHkvhvuZGI_ZTO8PGtiq5ntFL907fj7pH9SWOuz8Nk9t5X7rPPQ0ntQShuBYa89QKVU2cfmhQRoAogbmYs22gLetkR8ZQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03908681>
[ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03137494<http://secure-web.cisco.com/1XibXIDoYPELJ8Qmp8ylDzLuf8aUubO7-jyooiQCEf8a082UlM2DJiqW5LaFdKT1yQJbxTKlXm1N_dBVMT-orB0SEIbRxWaLJDGWLozzZ8D-UhNRaYXYgWHAzjvA6draUI0HwfhbOmcDglBW0Q06X4mOA2cCvheWHU-rDg5mA3PdplDBSiG6JmbgZg-feiB947xEiq2BUD8ZrJe9j8XTPhjYBed6n1I_4WbG9tNT1YNCCpzNtFjBtVwnO-NTCN4QbXB2UmoKnv8og7_XILbQrEg/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03137494> inCallFcnWithTrap+00000086
[ 35] 0x00007f2b225b3c0b /export/rel60_shadow/glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03677195<http://secure-web.cisco.com/1IAIH2i6-h19TW-GQXcC6sE7doC05sQYZagDqPgNU7ylypApwktFIOYKOoaKDLZKVt6j1FAmWztWJ2TpLtqqgQ_JPtZUaeDVOLW6CQR7hI9SuV0fizRPOBwBdGUHvBvKq2W35Tmj27nCuylilBfvIx_fAJmYZvwD8WFgDdLEl4sZmL812gt0QLdUyaJa5Av3bXoLMpCjFcB1nM8CY9SVYRn98cmJyTHQ5hRsVF0m8j3uzDgGf6cW5wRbtzDfQ2RQG8zgWtA8CAoUH_oMeziILfA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03677195>
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Exercise for Brain Health Lab
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dcallow@umd.edu<mailto:dcallow@gmail.com>
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------------------------------
Message: 4
Date: Fri, 28 May 2021 16:36:07 -0400
From: Daniel Davidson Callow <dcallow@umd.edu>
Subject: Re: [Freesurfer] Hippocampal Subfield error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAFMVdscRXD5BxWCG2RAJMCsN_VxUNvVb81=Vo5NsKpzKZuUcVw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Okay.
I tried the following file. HCA8133362_V1_MR.zip
ftp> put HCA8133362_V1_MR.zip
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.
ftp>
ftp> put HCA8133362_V1_MR.zip
200 PORT command successful. Consider using PASV.
553 Could not create file.
I am unsure if it was uploaded correctly. If so please look at the
Take a look at the hippocampal-subfields-T2-highres.log for the command
that failed. For some reason, the T2 and Highres versions seemed to work
for different subjects.
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcallow@umd.edu <dcallow@gmail.com>
443-254-6298
On Fri, May 28, 2021 at 4:10 PM Iglesias Gonzalez, Juan E. <
JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
> Please compress the whole subject directory and upload it to the ftp
> https://secure-web.cisco.com/17V8syWMVTKaaQhcS6MhcEk3ryPp1_XzTsJDwNhfnSpz5-qvlgwXye9h8Wsj7x3_zJeLzSMUfnEaJ8Ldw1zydmk8KhfVAankUo_IbE_zsAf8gLNkiRi8azFWqXuzO-lryPPpJkHys9g515JC0hcgmKgauj0MtTcD3AQKHQM3qSkJOyxE1U8RqxtApS3DCtnle9jb4xNv9jSwcB_CWJ106fC6zUaH4CWT1ZwEfHHCZSyQYREOeVnE-99eLF3-o3el6kA6jWnyaW23ZBAUTiaMCTA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFtpFileExchange
> Cheers,
> /E
>
> Juan Eugenio Iglesias
> Senior research fellow
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
> http://secure-web.cisco.com/1XIQD_seUELoMBl32vITG_77ibtO3YwKokZL9vz-PcxXYRKf3CfhTe9-zVIwpP0gO9cpwQY2C4871TrcCqjugL2aWgMRVvRNDJKGRV7gnceJnYmyG46kw49v-Fwb6BxqwRCRl8y7svy9w3AGhwSm62l7gv2mDj8d8Q_zLIsKzO1FfcpyTKrpNb8kW6SL7dyErUDRn2ALuoAkuFpVFc5Hig8jaSByrZYV5CtqnjQ9sSiAOkwqi7z3eij1-tn_auVTh4qiJvU0JV4ASqtLlZChaQA/http%3A%2F%2Fwww.jeiglesias.com
>
> On May 28, 2021, at 15:35, Daniel Davidson Callow <dcallow@umd.edu> wrote:
>
> External Email - Use Caution
>
> Sure, what is the best way to share it with you? and which folders/files
> should I send?
>
> On Fri, May 28, 2021 at 3:28 PM Iglesias Gonzalez, Juan E. <
> JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
>
>> It seems the linear registration is dying. Would you mind sharing the
>> subject, please?
>> 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/1XIQD_seUELoMBl32vITG_77ibtO3YwKokZL9vz-PcxXYRKf3CfhTe9-zVIwpP0gO9cpwQY2C4871TrcCqjugL2aWgMRVvRNDJKGRV7gnceJnYmyG46kw49v-Fwb6BxqwRCRl8y7svy9w3AGhwSm62l7gv2mDj8d8Q_zLIsKzO1FfcpyTKrpNb8kW6SL7dyErUDRn2ALuoAkuFpVFc5Hig8jaSByrZYV5CtqnjQ9sSiAOkwqi7z3eij1-tn_auVTh4qiJvU0JV4ASqtLlZChaQA/http%3A%2F%2Fwww.jeiglesias.com
>> <http://secure-web.cisco.com/1gT1t332MrjlumWoLsCvCODpcjL_Q7MljRoRdHSVXsW_jLPgjmaoLw7W3F0bWnNAuU_i6YcvUn1CduipTCLoLmI28KrJsxObJ-pJjn0aT42elUDeQDY-VOqdDAsm_XCSLk6O0cQQsHQZ_WeLdLkkSP0ZqAF22pxtjRYWOS_mGB4DgjcwDWt2LSx_Vl4dfFH7q6x0dS6wAUxGejm01T0GyOn03KUjtR1Y7XZ1AVi0U9kSfev4sOmBR8c1iZDmEC4jy_1ZRJ6fDyEI8ZlK8tFektA/http%3A%2F%2Fwww.jeiglesias.com>
>>
>>
>> On May 28, 2021, at 12:20, Daniel Davidson Callow <dcallow@umd.edu>
>> wrote:
>>
>> External Email - Use Caution
>>
>> Hello Juan,
>>
>> I am using data from the HCP aging dataset which has a T1 and a
>> high-resolution hippocampal scan (T2).
>>
>> Yes, it does seem that the T2 and T1's are roughly aligned to each other.
>> It seems like it has something to do with the creation of the
>> tmp/hippoSF_T1T2_v21_highres_left/ folder where the program is expecting
>> something to be produced that is not there/hasn't been produced.
>>
>> Again, here is an example of the code output/error.
>>
>> @ linenum = 1
>> cd /data/bswift-1/dcallow/aging/freesurfer
>> set subj= ( HCA8587705_V1_MR )
>> rm: No match.
>> rm -rf
>> /a/ha-nfs-2-ib/export/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/IsRunning.lh+rh
>> cd /data/bswift-1/dcallow/aging/freesurfer
>> echo HCA8587705_V1_MR
>> HCA8587705_V1_MR
>> segmentHA_T2.sh HCA8587705_V1_MR
>> /data/bswift-1/dcallow/aging/imaging/HCA8587705_V1_MR/unprocessed/TSE_HiResHp/HCA8587705_V1_MR_TSE_HiResHp.nii.gz
>> highres 1
>> #--------------------------------------------
>> #@# Hippocampal Subfields processing (T1+T2) left Fri May 28 12:05:35 EDT
>> 2021
>> ------------------------------------------
>> Setting up environment variables
>> ---
>> INFO: error loading libraries in default configuration, trying with MCR
>> libraries only
>> LD_LIBRARY_PATH is
>> .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswif$Registering
>> norm.mgz to additional volume
>> No more processes.
>> ERROR: could not open
>> /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh
>> for reading
>> ERROR: loading
>> /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh
>> as MGH
>> Warning: File
>> '/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh'
>> not found.
>> [^H> In myMRIread at 64
>> In segmentSubjectT1T2_autoEstimateAlveusML at 186]^H
>> Attempt to reference field of non-structure array.
>>
>> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 188)
>> MATLAB:nonStrucReference
>> @#@FSTIME 2021:05:28:12:05:35
>> run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 7.49 S 0.61 U 6.79 P
>> 98% M 283156 F 0 R 84320 W 0 c 2392 w 9596 I 0 O 85080 L 5$@#@FSLOADPOST
>> 2021:05:28:12:05:42 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
>> 60.45 53.15 38.08
>> Linux compute-4-33.bswift.umd.edu
>> <http://secure-web.cisco.com/1sqdwOUu2B9k20N1ZAF2G3AjMOwj2lJePh4GNFQiYhImRJsLReMbcU3SXEBp36HD81jqxGdU8a11rJylMhtgbY4fajAEU2pMYsr0DVpWBlkaOMa76fsceUrIl9aQQGsiXc4t6jAY6yGgeO2kzpjftDgTb1eWEbDGuGccb2HunIGkKRrj0yIIhMCUBXNMsPGxCpYhRthsOcBxVagqqmQZxB5PmjkPPc4BKyyMN_eLiZEjt4ui6aNQG76WiX_3leabsXT0Dc4AQ7eKoT8OWNqqHcQ/http%3A%2F%2Fcompute-4-33.bswift.umd.edu>
>> 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64
>> x86_64 x86_64 GNU/Linux
>>
>> T2 hippocampal subfields exited with ERRORS at Fri May 28 12:05:42 EDT
>> 2021
>>
>> For more details, see the log file
>> /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/hippocampal-subfields-T2.highres.log
>>
>>
>> Any ideas what might be causing this error. Again, it seems to be working
>> for a small subset of participants however, the majority are failing with
>> this error.
>> *Daniel Callow*
>> *PhD Student, Neuroscience and Cognitive Science*
>> Exercise for Brain Health Lab
>> University of Maryland, College Park
>> dcallow@umd.edu <dcallow@gmail.com>
>> 443-254-6298
>>
>>
>>
>> On Fri, May 28, 2021 at 9:32 AM Iglesias Gonzalez, Juan E. <
>> JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
>>
>> Dear Daniel,
>>>
>>> Are the T2s and T1s roughly aligned in RAS (physical coordinates)? In
>>> other words: do they (roughly) overlap when you open them together in
>>> Freeview?
>>>
>>> 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/1XIQD_seUELoMBl32vITG_77ibtO3YwKokZL9vz-PcxXYRKf3CfhTe9-zVIwpP0gO9cpwQY2C4871TrcCqjugL2aWgMRVvRNDJKGRV7gnceJnYmyG46kw49v-Fwb6BxqwRCRl8y7svy9w3AGhwSm62l7gv2mDj8d8Q_zLIsKzO1FfcpyTKrpNb8kW6SL7dyErUDRn2ALuoAkuFpVFc5Hig8jaSByrZYV5CtqnjQ9sSiAOkwqi7z3eij1-tn_auVTh4qiJvU0JV4ASqtLlZChaQA/http%3A%2F%2Fwww.jeiglesias.com
>>> <http://secure-web.cisco.com/1M43tYnBIwe0As03lwnAGcBzSZfvIXhP_UsjatHKyZUaaQ4wSAHDh_rwH1615JlqcHfPYywTwRzVbI_to9hVZq--leXJy2p4Zrh_mUI3lNII4SXa870Dh3HPFfDvztZQqR8Lzb5jZgrooucfAyVmWEBNMCuB8-mMhkfQpliBwpQ4AlrLgpwXKROaATxslozZ45t7me-SsaBv2pGfPGHhefMDQiyWYTTwRkiWX5UsaBqKv7GznpWuae2cijb7yGp0Ot534fYLsrPfsPuzrmK7NMQ/http%3A%2F%2Fwww.jeiglesias.com>
>>>
>>>
>>> On May 28, 2021, at 07:53, Daniel Davidson Callow <dcallow@umd.edu>
>>> wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Hello,
>>>
>>> I am running into errors when running
>>>
>>> segmentHA_T2.sh ${subj}
>>> /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
>>>
>>> Approximately 10% of my subjects are being processed but for some
>>> reason, the majority fail to execute. Here is an output from the error log.
>>> ------------------------------
>>> USER dcallow
>>> HOST compute-4-32.bswift.umd.edu
>>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
>>> PROCESSID 4033
>>> PROCESSOR x86_64
>>> OS Linux
>>> Linux compute-4-32.bswift.umd.edu
>>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu> 2.6.32-754.35.1.el6.x86_64
>>> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>>> ------------------------------
>>>
>>> #--------------------------------------------
>>> #@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51
>>> EDT 2021
>>> ------------------------------------------
>>> Setting up environment variables
>>> ---
>>> INFO: error loading libraries in default configuration, trying with MCR
>>> libraries only
>>> LD_LIBRARY_PATH is
>>> .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering
>>> norm.mgz to additional volume
>>> makeIsotropic WARNING: not different enough, won't reslice!
>>> No more processes.
>>> ERROR: could not open
>>> /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
>>> for reading
>>> ERROR: loading
>>> /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh
>>> as MGH
>>> Warning: File
>>> '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh'
>>> not found.
>>> [^H> In myMRIread at 64
>>> In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H
>>> Attempt to reference field of non-structure array.
>>>
>>> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211)
>>>
>>>
>>>
>>> MATLAB:nonStrucReference
>>> @#@FSTIME 2021:05:27:21:39:51
>>> run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61
>>> P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST
>>> 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
>>> 31.22 29.74 28.95
>>> Linux compute-4-32.bswift.umd.edu
>>> <http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu> 2.6.32-754.35.1.el6.x86_64
>>> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT
>>> 2021
>>>
>>> I am also getting a matlab_crash_dump file
>>>
>>> ------------------------------------------------------------------------
>>> Segmentation violation detected at Thu May 27 21:51:52 2021
>>> ------------------------------------------------------------------------
>>>
>>> Configuration:
>>> Crash Decoding : Disabled
>>> Current Visual : None
>>> Default Encoding : US-ASCII
>>> GNU C Library : 2.12 stable
>>> MATLAB Architecture: glnxa64
>>> MATLAB Root : /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux
>>> <http://secure-web.cisco.com/1zf_ot3cQGUvMhTgphfJ7towMivhNxWKqA3AayyU_OPHHiMasb-EvBGTFN3sYYJDfq2OTyGKzBZ_szFAJCXZHlZGEtJjl-Jdhb4Q1bIAonDtiewkPoyMXUpsAcQaKfsBE0RsmUc-YGdemu96LMj476x2UIb3GfDNjDVx7ULnA6ydsfS5RHTfxedRiKFt6oLIZ-8AmzrNc44dziwIEz2Tm1zVXkZba_ISfg8fwql2KxoL8WGjCE7_3XIDrEbE-HNmMPhnNu3asRalw0_AJ6BOTkA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux>
>>> MATLAB Version : 8.4.0.150421 (R2014b)
>>> Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May
>>> 29 04:45:43 EDT 2020 x86_64
>>> Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
>>> Software OpenGL : 0
>>> Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java
>>> HotSpot(TM) 64-Bit Server VM mixed mode
>>> Window System : No active display
>>>
>>> Fault Count: 1
>>>
>>>
>>> Abnormal termination:
>>> Segmentation violation
>>>
>>> Stack Trace (from fault):
>>> [ 0] 0x00007f2b30f06213
>>> /lib64/libpthread.so.0+00033299 pthread_join+00000035
>>> [ 1] 0x00007f2a9f4d847d
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 2] 0x00007f2a9f4d8cac
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 3] 0x00007f2a9f5cae63
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 4] 0x00007f2a9f5af896
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 5] 0x00007f2a9f5a6b8d
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 6] 0x00007f2a9f5a6fd0
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 7] 0x00007f2a9f5aad00
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 8] 0x00007f2a9f5a5c3c
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 9] 0x00007f2a9f44fb03
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 10] 0x00007f2a9f42b9cc
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 11] 0x00007f2a9f42b132
>>> /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
>>> 12] 0x00007f2b21dcfc0a /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538
>>> <http://secure-web.cisco.com/15wmunFtJy8RzDq9oVQoOhvMj4SqFWIMICnRxUk7kN3uyYtej40W1KAf2FgN8p-YHhCe94AM96CLuzs2_pg0h5a-wPhOcAbQDBbn9UroNugqM9zMNW_x85lUFfPpgR5eVTK_sVWwcg4CiDnJkgZm34QYRBZBTcAYN9riNJ9m1rpj4PKAxhbRXEmUfM_1qcroQ-tCUoHaYthJ1wh2oe_rXJu65oN57rZkO5uN2D-kO6NX50rAL6N-yYqFbQTvlWSoqZXcpaDvh0nH11oRbZSCgYQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmex.so%2B00150538>
>>> mexRunMexFile+00000090
>>> [ 13] 0x00007f2b21dcc5c4 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00136644
>>> <http://secure-web.cisco.com/1VNIP2TP7g_-k-V3EXmoqH3gSLCQPAVKDrJmmFHk4DSCIs8dpaPhlMZY3o1R2Gcl45b59huNzCHAuDXy3Jk_DTzSHWeoAdTGEyyL_kxblZnIJkrmRuC21lPT3uRUUA5F-hhCNI4L1ewaawelx52Ns4n9o9ra_oWhRf9AD84pTyjJnXGVX1FrlCKhr8xCI3BxucHGenwthYaUBlmin56HnLgin-otSEMgaMDZVIlfwdsJjpm_sB9ATY4IgK9GI4jaKI7g9MMLbHjEVqHgacPW6sw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmex.so%2B00136644>
>>> [ 14] 0x00007f2b21dcd414 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00140308
>>> <http://secure-web.cisco.com/1DHyyF-k0XGkPk9gRiFdvyrzyhAwZmrJ8Vpas5l1bhBSmDpXf1DE5cQ_3mHR9xgFvggvUyK6nS-KPKUap_Y3PtkQxvO-b174nhgWgkAkhqF0GCz9M2ffTgT-YPppDR2yc8dr-rFkMth1BYS8tXsV0l1UcZ8aP_QkA_xu_XEQ-IULq2naXsfdbIOmnONEUC_6gpFEpp2_EkJr0prYDw63-Fcx2DNkGKP9H_lYz9w8au_3bwu-8Upbm2dSza-8ykxGxxKbsp1J3VugjWqfirkKTxg/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmex.so%2B00140308>
>>> [ 15] 0x00007f2b232ff329 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>>> <http://secure-web.cisco.com/1YvAiBC_3G9VAawE4steKXeCaNTlrpgMnQG_qhwLeycblS635IsShf_UEZVAtvWU98ic7nFoyTObuenzWyfIOrdZ1ukAI2_Rwpr7BFODPD8xr8FVnAIglj8lndurD-18acdOLCAx9cl__2Xe2_21LZQn4auLKXubsYP6cvn7ODCEtX6tup_3H0vUFEZ4WQGRknJISa7pBZBc8A0cMb8ooCFDVafzDFjkSj4EiKd-9hl01YeUQPAu5Hwt6s7FUSKNmxksu_SyBfaeCpYE8OvqpHA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_dispatcher.so%2B00791337> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[
>>> 16] 0x00007f2b2260fb70 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
>>> <http://secure-web.cisco.com/1FqlnK1mbYe0fc4WrLh27McIgFcpF4caZpprfvWHGIiLLoxXo6_L3M8BINfHY5-jSh1ngRLTREAlaV-ecKWLXgaZmAvPaE1WcZ3K8NB0Vvxh-3_asNJndl8j3D5yqTCWCZygCAlsQE2BScTJzzzgOg0nDdICKmBjoe5NmIpTDU8e12QBMlVY4gLY59bk2WU5NEVeEhnmukrN_bzXIchegVXLsx6fumnKQzIoSHTfUwa7LAM4D8pzDWBH7hsRyezlzADNhYYUpmOqNOqn5JFOEDA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04053872>
>>> [ 17] 0x00007f2b225bfe02 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
>>> <http://secure-web.cisco.com/1oFCMQbMq8_LNNSwavId3uL9KorlKBV-Dq9AH2k9--Ptuwe56v1f0M8oNm9UBgRvAQacl9RKg1Qg0DY7ko-IcvfQe-2sfN0qRBoXdPr8AINOFM5HQFjasYlRzdVlc-G_JqKNPbJEzsVRjfXLn9CA4BIE2htjH6A3_wsQTimZoAzJF_HNTmhJ7qA5E1fFaDN7kOubeJKvBSvnuTwu-bMBUREZA03ALLxwcXdU7Zf9awXp32KrUJr3sssPhgqjOZm0-uLmk2eWzYlnYg6SD7XCpag/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03726850>
>>> [ 18] 0x00007f2b225c2022 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
>>> <http://secure-web.cisco.com/1mkHocgN-E2JcT6SI0pNs-oXMVy5k5oGB6gATPm9NI82pijbaPsiS_mVu6yD_8ldltWLoJH4dyPp4vYVPvfXnMD03lmxENx9NH-5f5d00CK147UzH945ZVfrdnKRmxtQZPQAbtHNrwjMC7s4lNIqHSR7GSaetK6V29YMKzu_-Tu1SwwBDg3JePYZjvodQRdYUkHEfs8YmahPAtNRQPM3MskmCOUcjL4tV6sdY1yfjwhrpmPrjlQKVXgKZQMDqosdS_VLmyb6B_maYrhrDgnW0aA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03735586>
>>> [ 19] 0x00007f2b225c7f87 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
>>> <http://secure-web.cisco.com/1IXEh5f9oNhkKzllddjiYB3PrZZ0_a0EZYlGzFTPY7IyKerNHNEwXaFMOYZXMm4hct0Rom3hL_ou_TGy8UJSc7P-OrfKK0CrXSeDSR-7YEwoHUr9hq-a_cceHo-B4JS3oLxWaU0ykCPBleBOrFVoTgQHmHnKJTjxDY5GAIqCi48jEIy7iuEXH8AMIgvxL5dbjDgjN_qtXvhWG70-bIbaIS0j25znSUF0ho6j9W7Q-okSGwCZJ0YkWBJerVuCH5b3o_Rr2u-KSeDxXNKED0dtlBw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03760007>
>>> [ 20] 0x00007f2b225c36ff /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
>>> <http://secure-web.cisco.com/1z7kRHrPDXQ2J89IxYNotG6f3AWl-VlFzlspUBbkrsL1gDgJbVg7Jvui01VXzy_9XgOLBM7uiNrNy2emqwnaZRVr97UmD81gSG0_F-eUpsqBkSrR3o5bOkcSlKSKbnIJLwrb7IlUi1lGu-eqqDsDfvtd8bmEZ9LWhsNqU63v-ByjHg8-Tppp8IHXCegbHJwtiYG5b7ldmmACZL3zXlOMT5m_Xf7vUxnL9hQ9AOVduNe9rwSJml83zaACIYRO7148iHaaWASzcChMIFktUQdn6DA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03741439>
>>> [ 21] 0x00007f2b225c4334 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
>>> <http://secure-web.cisco.com/1Qidv5KKgCpV0A4yNcjeOaCG5BbPEneNCG_VGPSEeihppLC0K8VCKQKqgycrF_JG7hDWxESiIkJ0zZSKIoEcr9MBBq-zCjGrXAT3o-uxNgPfkPx2Diq5rB4I4Nj_5SOHSz67iis8FUiswPfla7T1ax5dsZbZqWNZzf3mRlN9H7qfLp7x9gNQlbo1DsK8hFvHTUGz_PM_4onSpO9CffOK0BfVEfeOpXOHy6EjznUeUWhuJyx6dorWoftGwaDXEKw44ZGcYPHdtnJXKpRfHp8TKpw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03744564>
>>> [ 22] 0x00007f2b2263952e /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
>>> <http://secure-web.cisco.com/1LFwdsCWta1IKYv3k3YydtSX7z6ZkdwRsguf-SFigI8Kxt4X2FK9QjJHavPcu2kTMH1M8_iHldk2sCDW-6Cw6fokp46WGvsOCfyh25z_jqednT1Bw_Rij1zigZ9QCabcdCHHrRmXYLySPYEVnuaTn22efOadhUo6Nk4TlR0yJ9IkLdzQFrQh_3bCoEoX8T_dZVAmOpLbfqeCTnXHh06TvfZx3I9xWFZvsuURivUTNG_DPyZpHm1y05pMXl4mY_b6ff5sdtFbOIGeh7kop0ZDDEw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04224302>
>>> [ 23] 0x00007f2b232ff329 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>>> <http://secure-web.cisco.com/1YvAiBC_3G9VAawE4steKXeCaNTlrpgMnQG_qhwLeycblS635IsShf_UEZVAtvWU98ic7nFoyTObuenzWyfIOrdZ1ukAI2_Rwpr7BFODPD8xr8FVnAIglj8lndurD-18acdOLCAx9cl__2Xe2_21LZQn4auLKXubsYP6cvn7ODCEtX6tup_3H0vUFEZ4WQGRknJISa7pBZBc8A0cMb8ooCFDVafzDFjkSj4EiKd-9hl01YeUQPAu5Hwt6s7FUSKNmxksu_SyBfaeCpYE8OvqpHA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_dispatcher.so%2B00791337> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[
>>> 24] 0x00007f2b2260fb70 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
>>> <http://secure-web.cisco.com/1FqlnK1mbYe0fc4WrLh27McIgFcpF4caZpprfvWHGIiLLoxXo6_L3M8BINfHY5-jSh1ngRLTREAlaV-ecKWLXgaZmAvPaE1WcZ3K8NB0Vvxh-3_asNJndl8j3D5yqTCWCZygCAlsQE2BScTJzzzgOg0nDdICKmBjoe5NmIpTDU8e12QBMlVY4gLY59bk2WU5NEVeEhnmukrN_bzXIchegVXLsx6fumnKQzIoSHTfUwa7LAM4D8pzDWBH7hsRyezlzADNhYYUpmOqNOqn5JFOEDA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04053872>
>>> [ 25] 0x00007f2b225bfe02 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
>>> <http://secure-web.cisco.com/1oFCMQbMq8_LNNSwavId3uL9KorlKBV-Dq9AH2k9--Ptuwe56v1f0M8oNm9UBgRvAQacl9RKg1Qg0DY7ko-IcvfQe-2sfN0qRBoXdPr8AINOFM5HQFjasYlRzdVlc-G_JqKNPbJEzsVRjfXLn9CA4BIE2htjH6A3_wsQTimZoAzJF_HNTmhJ7qA5E1fFaDN7kOubeJKvBSvnuTwu-bMBUREZA03ALLxwcXdU7Zf9awXp32KrUJr3sssPhgqjOZm0-uLmk2eWzYlnYg6SD7XCpag/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03726850>
>>> [ 26] 0x00007f2b225c2022 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
>>> <http://secure-web.cisco.com/1mkHocgN-E2JcT6SI0pNs-oXMVy5k5oGB6gATPm9NI82pijbaPsiS_mVu6yD_8ldltWLoJH4dyPp4vYVPvfXnMD03lmxENx9NH-5f5d00CK147UzH945ZVfrdnKRmxtQZPQAbtHNrwjMC7s4lNIqHSR7GSaetK6V29YMKzu_-Tu1SwwBDg3JePYZjvodQRdYUkHEfs8YmahPAtNRQPM3MskmCOUcjL4tV6sdY1yfjwhrpmPrjlQKVXgKZQMDqosdS_VLmyb6B_maYrhrDgnW0aA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03735586>
>>> [ 27] 0x00007f2b225c7f87 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
>>> <http://secure-web.cisco.com/1IXEh5f9oNhkKzllddjiYB3PrZZ0_a0EZYlGzFTPY7IyKerNHNEwXaFMOYZXMm4hct0Rom3hL_ou_TGy8UJSc7P-OrfKK0CrXSeDSR-7YEwoHUr9hq-a_cceHo-B4JS3oLxWaU0ykCPBleBOrFVoTgQHmHnKJTjxDY5GAIqCi48jEIy7iuEXH8AMIgvxL5dbjDgjN_qtXvhWG70-bIbaIS0j25znSUF0ho6j9W7Q-okSGwCZJ0YkWBJerVuCH5b3o_Rr2u-KSeDxXNKED0dtlBw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03760007>
>>> [ 28] 0x00007f2b225c36ff /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
>>> <http://secure-web.cisco.com/1z7kRHrPDXQ2J89IxYNotG6f3AWl-VlFzlspUBbkrsL1gDgJbVg7Jvui01VXzy_9XgOLBM7uiNrNy2emqwnaZRVr97UmD81gSG0_F-eUpsqBkSrR3o5bOkcSlKSKbnIJLwrb7IlUi1lGu-eqqDsDfvtd8bmEZ9LWhsNqU63v-ByjHg8-Tppp8IHXCegbHJwtiYG5b7ldmmACZL3zXlOMT5m_Xf7vUxnL9hQ9AOVduNe9rwSJml83zaACIYRO7148iHaaWASzcChMIFktUQdn6DA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03741439>
>>> [ 29] 0x00007f2b225c4334 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
>>> <http://secure-web.cisco.com/1Qidv5KKgCpV0A4yNcjeOaCG5BbPEneNCG_VGPSEeihppLC0K8VCKQKqgycrF_JG7hDWxESiIkJ0zZSKIoEcr9MBBq-zCjGrXAT3o-uxNgPfkPx2Diq5rB4I4Nj_5SOHSz67iis8FUiswPfla7T1ax5dsZbZqWNZzf3mRlN9H7qfLp7x9gNQlbo1DsK8hFvHTUGz_PM_4onSpO9CffOK0BfVEfeOpXOHy6EjznUeUWhuJyx6dorWoftGwaDXEKw44ZGcYPHdtnJXKpRfHp8TKpw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03744564>
>>> [ 30] 0x00007f2b2263952e /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
>>> <http://secure-web.cisco.com/1LFwdsCWta1IKYv3k3YydtSX7z6ZkdwRsguf-SFigI8Kxt4X2FK9QjJHavPcu2kTMH1M8_iHldk2sCDW-6Cw6fokp46WGvsOCfyh25z_jqednT1Bw_Rij1zigZ9QCabcdCHHrRmXYLySPYEVnuaTn22efOadhUo6Nk4TlR0yJ9IkLdzQFrQh_3bCoEoX8T_dZVAmOpLbfqeCTnXHh06TvfZx3I9xWFZvsuURivUTNG_DPyZpHm1y05pMXl4mY_b6ff5sdtFbOIGeh7kop0ZDDEw/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B04224302>
>>> [ 31] 0x00007f2b232ff329 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
>>> <http://secure-web.cisco.com/1YvAiBC_3G9VAawE4steKXeCaNTlrpgMnQG_qhwLeycblS635IsShf_UEZVAtvWU98ic7nFoyTObuenzWyfIOrdZ1ukAI2_Rwpr7BFODPD8xr8FVnAIglj8lndurD-18acdOLCAx9cl__2Xe2_21LZQn4auLKXubsYP6cvn7ODCEtX6tup_3H0vUFEZ4WQGRknJISa7pBZBc8A0cMb8ooCFDVafzDFjkSj4EiKd-9hl01YeUQPAu5Hwt6s7FUSKNmxksu_SyBfaeCpYE8OvqpHA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_dispatcher.so%2B00791337> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[
>>> 32] 0x00007f2b225ecbf0 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03910640
>>> <http://secure-web.cisco.com/1XY2HS1eoFmCZj_0FLnEggB0qkNY41bJhNhIxrQkYQlfUUFOeH7A1s1kvm8DQWM0JlgCJOvl0vJiumfWqWZpNqcPopcWLIVMrGP89FTG4LxSpueiRrp0XpSeQ-vDq_Gp62up2g5nwwIVcmd7-oGNZmWQzFkkViXG0-KZbB3pU0t5L9QDBRtqK8nLjqVkLlKjqncDvdWTxmejTP9mpEj20zQuBbn_-88xbgdpbszqvtvKEThIjeHxG57d1SeK3JuQLoJ9FFtxjVfLmaIa15EmzgQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03910640>
>>> [ 33] 0x00007f2b225ec449 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03908681
>>> <http://secure-web.cisco.com/15RN_eXEIUAO_WqqYNIIAMljnNJvT34HmTcfAnwdPgjQ5Zs_ljlxOt3x13LTRvM7d5IunUlOUz5aKZ7GubCOSwKdOyfM_N8vvu2s8rcvMi_VSMoOHrf9PjqE-VmSGbzKW0i_9a6AXA6ZDjAeKelV7RTipDEECT6fzvwMMYPf94nguZ7fEEF4bMoM2nZHkvhvuZGI_ZTO8PGtiq5ntFL907fj7pH9SWOuz8Nk9t5X7rPPQ0ntQShuBYa89QKVU2cfmhQRoAogbmYs22gLetkR8ZQ/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03908681>
>>> [ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03137494
>>> <http://secure-web.cisco.com/1XibXIDoYPELJ8Qmp8ylDzLuf8aUubO7-jyooiQCEf8a082UlM2DJiqW5LaFdKT1yQJbxTKlXm1N_dBVMT-orB0SEIbRxWaLJDGWLozzZ8D-UhNRaYXYgWHAzjvA6draUI0HwfhbOmcDglBW0Q06X4mOA2cCvheWHU-rDg5mA3PdplDBSiG6JmbgZg-feiB947xEiq2BUD8ZrJe9j8XTPhjYBed6n1I_4WbG9tNT1YNCCpzNtFjBtVwnO-NTCN4QbXB2UmoKnv8og7_XILbQrEg/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03137494>
>>> inCallFcnWithTrap+00000086
>>> [ 35] 0x00007f2b225b3c0b /export/rel60_shadow/
>>> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03677195
>>> <http://secure-web.cisco.com/1IAIH2i6-h19TW-GQXcC6sE7doC05sQYZagDqPgNU7ylypApwktFIOYKOoaKDLZKVt6j1FAmWztWJ2TpLtqqgQ_JPtZUaeDVOLW6CQR7hI9SuV0fizRPOBwBdGUHvBvKq2W35Tmj27nCuylilBfvIx_fAJmYZvwD8WFgDdLEl4sZmL812gt0QLdUyaJa5Av3bXoLMpCjFcB1nM8CY9SVYRn98cmJyTHQ5hRsVF0m8j3uzDgGf6cW5wRbtzDfQ2RQG8zgWtA8CAoUH_oMeziILfA/http%3A%2F%2Fglue.umd.edu%2Fsoftware%2Fmatlab%2F2014b%2FLinux%2Fbin%2Fglnxa64%2Flibmwm_interpreter.so%2B03677195>
>>>
>>> This error was detected while a MEX-file was running. If the MEX-file
>>> is not an official MathWorks function, please examine its source code
>>> for errors. Please consult the External Interfaces Guide for information
>>> on debugging MEX-files.
>>>
>>> If 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://secure-web.cisco.com/1rdnPKCDuyhiu30H52s9OAw_MLOLTJaFfywoYqY9AKfmYbrcqJPMzk0Zr39eMCcEhoZNAxerEI7CIen4F1ol1hYrFirBG0r1ZqQDazKtbBdanYw5h_zZfGFuDDx1r1SNV3me9yoBFpac2nJ84QNSGFMcynYImwlhuuLKr1ugfd_Lbcq2vvrALiwRHVpNzX4tT7yTCGfPvo5fDmj9tloVhk-rjOS1nS_L6HnkLq94JtpkNtaOAeMbYy0Ur6WJKjxo98JPzeZhlQqNgWUUrRih76A/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
>>> <http://secure-web.cisco.com/1B8en4WQVOmBM-TonUpSzamw674QdqjI_ltVT2KdTcbPbuPW0K3Ay8KDhD5c4RCuwKYVmR07FjU0Aevx09ahCMeyv0JkXQ52Hmhwb4sx7s4JboH2NUrlUAj_t1NiR1NWXsdcBbrW2ARL_QZIvDtzEvCZllOY4TGkavTAZNKXychD1QqvsZFE-MKZXZcrP5pagoPPejJGw9gWjGYxJHuPexjzzMvAZ00KWwGungv_lBCKCFbVfyIShsbLN-xOO4h3eWRUjCNBh0HGJu8phyXt6Xg/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F>
>>>
>>> A technical support engineer might contact you with further information.
>>>
>>> Any insight or help you can provide is greatly appreciated.
>>> *Daniel Callow*
>>> *PhD Student, Neuroscience and Cognitive Science*
>>> Exercise for Brain Health Lab
>>> University of Maryland, College Park
>>> dcallow@umd.edu <dcallow@gmail.com>
>>> 443-254-6298
>>>
>>> _______________________________________________
>>> 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/1RGSnHGed1XqM0RkhyPBHHITWtu_lHqadhPUwOiojpwsq5SHkjdBlOJ3t0X82-Ji98CAThmlaS69vZLZ0GnUk4QILvSdehVcUNJexOpT17lJOkVC3q6AcO0v492L46QfWmTMVwJnSWYHn3XZEpPrSProxVeI3JPExQgdXvbfSPAx0WFBbUYPbnhbT-ZAKbmdpYJ9wFY9wxx9ElPQiCNFJwX_2_1LlMkjh24gkxE1FgVhduErzfHwxwfeZWDJSO1Gpg9RkSGG9VY1lXJKRloIHdQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>> <https://secure-web.cisco.com/1A8bx9DXo139MZ9fUyweH53j6yZXrv_4CRKnXmAPk9kBzduToxLkj1vZWvmLonEsFp84m6XFRXlYrhqS8cUoh9IzqRFztAI5adQtTo4Iy_XLJDMVWzFhr8eviVP41cbGOZYMq4fcW46zm8_oSEJfCriPqueW-7MMEvbUq6BQ_zYUYkkXKjDakz6kwHoc8IM-ImrVAC_5g5u6nyFnCsRuLDqZXtJtna2vk0JoJ1JKnG0u-uOddmpFE6_Lq7iVk3qSNH1AezDonJ0zHgMvrnYxrCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>>
>>>
>>> _______________________________________________
>>> 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/1RGSnHGed1XqM0RkhyPBHHITWtu_lHqadhPUwOiojpwsq5SHkjdBlOJ3t0X82-Ji98CAThmlaS69vZLZ0GnUk4QILvSdehVcUNJexOpT17lJOkVC3q6AcO0v492L46QfWmTMVwJnSWYHn3XZEpPrSProxVeI3JPExQgdXvbfSPAx0WFBbUYPbnhbT-ZAKbmdpYJ9wFY9wxx9ElPQiCNFJwX_2_1LlMkjh24gkxE1FgVhduErzfHwxwfeZWDJSO1Gpg9RkSGG9VY1lXJKRloIHdQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>> <https://secure-web.cisco.com/1A8bx9DXo139MZ9fUyweH53j6yZXrv_4CRKnXmAPk9kBzduToxLkj1vZWvmLonEsFp84m6XFRXlYrhqS8cUoh9IzqRFztAI5adQtTo4Iy_XLJDMVWzFhr8eviVP41cbGOZYMq4fcW46zm8_oSEJfCriPqueW-7MMEvbUq6BQ_zYUYkkXKjDakz6kwHoc8IM-ImrVAC_5g5u6nyFnCsRuLDqZXtJtna2vk0JoJ1JKnG0u-uOddmpFE6_Lq7iVk3qSNH1AezDonJ0zHgMvrnYxrCA/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://secure-web.cisco.com/1UQ1Y9yewaFDq047VMbNCsHFEPFAxKXRHEkfpe5unW_UyexpBQUaqBY7z5QbRVfiQ_JxNFBrT1jxximPhWhH-eLdP-t_o4ZuIR2nEvUOGC9iNa5FhsLTO8Y3PeySFgIfAW_0HhihsSu9x3vBLQKs4dguE4sMMhpJYD0bBw0ad6UqmsCyhXc8bzAxiWUEZcKzlwZM7ounMn7-Hna_FTHqKBFONMm9Kvt7R5Br9nZZzBXj1VK2TfkMugzPIW4yur0mYD8U_S_kon72SAuKy6Spq2w/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>> <http://secure-web.cisco.com/1kXgL-61ri7LvFmAdiWTLJybvYn_lfanoeiv2-s7_Rk5FDIaevnnh-NYCX5gpAGj8lzXkPVvDBQcLqwsMrjJI5q9vityomxCQDuKBXLNWj6XY81Z9AH_qummfiWzH6d4fjKjCbAexi662jc5CT099BpWJe1ctL2GCRrDW8CnDwR56nGnUPtUBXr_KDTsyxahBR5sk_REEBN3qbidJtSUm25iEPvOZ64fSGHxgeVf8R9kMCPIZQuIbboBWYYxhACFZ_ZiqIFS_yrsyP5pGCWFl5A/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
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1RGSnHGed1XqM0RkhyPBHHITWtu_lHqadhPUwOiojpwsq5SHkjdBlOJ3t0X82-Ji98CAThmlaS69vZLZ0GnUk4QILvSdehVcUNJexOpT17lJOkVC3q6AcO0v492L46QfWmTMVwJnSWYHn3XZEpPrSProxVeI3JPExQgdXvbfSPAx0WFBbUYPbnhbT-ZAKbmdpYJ9wFY9wxx9ElPQiCNFJwX_2_1LlMkjh24gkxE1FgVhduErzfHwxwfeZWDJSO1Gpg9RkSGG9VY1lXJKRloIHdQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1jsYurSjDkGLI1-FXY0m-g6eynNSH2B64GSTOT1rHMjSjL7kIkfgKV2zmlJPeBvA-TEVNAom0uKRZNC6T9sZBy14KcgdYWMVG7kY74X1XiBBJsat99Dd13x0rDvSPQ_ZsHdqjh5k7NEgH53EIs3OyAPn3u1TEOQiO9Jc1HlBv8y_Xv-Fw4rjHlXw5_LtjitzefDiVcas7hloDVAV6zNI93mxW9z-Kp8TebW8Mv_BjZtcCRAvCi0yWr_6yADWQB6IwNjyBDeNCbzrmb8_Q0XVVFQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
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> --
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> dcallow@umd.edu <dcallow@gmail.com>
> 443-254-6298
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Message: 5
Date: Sat, 29 May 2021 03:14:25 -0300
From: Di?genes Bispo <diogenesdiego@gmail.com>
Subject: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with
--csd-out)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAPPOJ6Mm3Niabu=MHW-+cJJcKt5+LmTdPYthiw=G6k80ovWybA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Freesurfer team.
I made the following command:
#!/bin/tcsh
setenv study $argv[1]
foreach hemi (lh rh)
foreach smoothing (10)
foreach meas (volume)
mris_preproc --fsgd FSGD/{$study}.fsgd \
--cache-in {$meas}.fwhm{$smoothing}.fsaverage \
--target fsaverage \
--hemi {$hemi} \
--out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh
end
end
end
----
#!/bin/tcsh
set study = $argv[1]
foreach hemi (lh rh)
foreach smoothness (10)
foreach meas (volume)
mri_glmfit \
--y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \
--fsgd FSGD/{$study}.fsgd dods \
--C Contrasts/Contrast-1_group.diff.mtx \
--C Contrasts/Contrast-2_group-x-age.mtx \
--C Contrasts/Contrast-3_group-x-icv.mtx \
--C Contrasts/Contrast-4_group-x-age-x-icv.mtx \
--C Contrasts/Contrast-5_GCCV.intercept.mtx \
--C Contrasts/Contrast-6_GCCV.age.mtx \
--surf fsaverage {$hemi} \
--cortex \
--glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \
--eres-save
end
end
end
----
#!/bin/tcsh
setenv study $argv[1]
foreach meas (volume)
foreach hemi (lh rh)
foreach smoothness (10)
foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
mri_glmfit-sim \
--glmdir {$dir} \
--grf 2.0 neg \
--cwp 0.05 \
--2spaces \
end
end
end
end
I have the following error:
...
mri_surfcluster --in
rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask
rh.volume.covid.10.glmdir/mask.mgh --cwsig
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh
--sum
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary
--ocn
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh
--no-fixmni --csd-out
rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd
--fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign neg
--oannot
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot
--bonferroni 2 --surf white
ERROR: need --csd with --csd-out
How should I proceed to solve this problem?
Thanks
Di?genes Bispo
diogenesdiego@gmail.com
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------------------------------
Message: 6
Date: Sat, 29 May 2021 10:23:03 +0300
From: Antti Cajanus <acajanus@gmail.com>
Subject: [Freesurfer] Group comparison with MD
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <CF11079F-8138-4E9E-A03F-E44B99276A5E@gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Freesurfer experts,
I?m trying to do a group comparison of cortical mean diffusivity. The study subjects form 2 groups (demented vs. non-demented). I?ve run recon-all and dt_recon on all of my study subjects. My goal is to create a surface, that has the mean diffusivity values sampled from the midpoint of the cortical thickness (50% the distance between WM and pia). I?m puzzled about three things;
1) Can I use the adc.nii created by dt_recon to represent the mean diffusivity or should I use something else?
2) Can I obtain the MD values from the midpoint of cortical thickness using mri_vol2surf command, using the optional ??projfrac 0.5? flag? i.e. mri_vol2surf ?src adc.nii.gz --out adc-to-midthick.mgz --hemi lh --projfrac 0.5 --srcreg register.dat
3) I want to smooth the the data with FWHM 15mm. Should I apply the smoothing in the mri_vol2surf (as registering the adc.nii to cortical ribbon) or in the mri_surf2surf phase (as registering the adc-to-midthick.mgz to fsaverage)?
Thank you already in advance!
Best,
Antti Cajanus
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