Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Trouble with creating surface of macaque brain
by Singh, Shridhar (NIH/NEI) [C] 27 May '21

27 May '21

External Email - Use Caution Hi, I am trying to create a surface of a macaque brain, but I am running into issues with white matter. I segmented the white matter and manually edit wm.mgz, however the surf/?h.white output of recon all is not outlining everything in wm.mgz, creating problems with the surface. I attached an image demonstrating the problem. The red is wm.mgz and the yellow outline is lh.white. Why would regions identified as white matter in the left hemisphere of wm.mgz not be recognized as white matter in surf/lh.white, and what could I do to fix this issue? Also, when I run recon-all with the -autorecon2-wm flag, it seems that all my edits are reversed in wm.mgz. wm.seg.mgz is created by mri_segment, and then during mri_pretess, wm.mgz reverts back to what it was before my manual edits. Is there something wrong? Here's how I call recon-all: recon-all -autorecon2-wm \ -subjid ${subj} \ -cc-crs ${CC_string} \ -pons-crs ${PONS_string} \ -noaseg \ -xopts-use Thanks, Shridhar Singh

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Cerebellum Masks
by Erik O'Hanlon 27 May '21

27 May '21

External Email - Use Caution Dear Experts, Is it possible to use the SUITS labels (#601-628) in the LUT to make masks and extract volume measures. I ultimately want to use the masks for tractography purposes. Can I use the mri_extract to pull out the specific ROI's and if so do I use it with aparc+aseg file. Any details and guidance would be very much appreciated. Thanks Erik

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recon-all fails in Freesurfer7.1 on docker
by Lara Foland-Ross 26 May '21

26 May '21

External Email - Use Caution Hello, I'm trying to run Freesurfer7.1 on docker. I have a macbook air with an apple chip with BigSur as the OSX. To test out the installation, I ran recon-all on bert: recon-all -all -s bert The command quits with this error: "ERROR: cannot determine file type for /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz Linux 8c70180fb77b 5.10.25-linuxkit #1 SMP PREEMPT Tue Mar 23 09:24:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon May 10 16:50:51 UTC 2021" I'm attaching the recon-all.log file. Could you please advise on how to troubleshoot? Many thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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Running recon-all on dicom/IMA files within the same study
by Nathan Hostetler 26 May '21

26 May '21

External Email - Use Caution Hi FreeSurfer devs, Thanks for the program! I am assisting in a study comparing structural neuroimaging data between groups. Some of the MRI files exist as .dcm, while others exist as .IMA. Given the variability in FreeSurfer outputs noted here: https://secure-web.cisco.com/1_vxoF_SONV8dZuTkJbocobHWUZzyYP1cLrpyTK0qXC1WT…, is it a sound practice for me to run recon-all on both dicom and IMA files within the same study? Or should I convert all files to NIFTI, and run analyses on those files (to eliminate the potential influence of filetype on output)? I only ask because I've already run recon-all on quite a few IMA files, and would have to re-do these scripts if it's better for me to convert to nifti first. I look forward to your response, and thanks again for all the work that you lot do! Nate

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Re: [Freesurfer] Multiple Versions Installed
by fsbuild 25 May '21

25 May '21

External Email - Use Caution If on the Mac you use the *.pkg file  (or on linux the *.rpm) installers, then different versions of freesurfer will be installed automatically under a directory with the appropriate version number, e.g., on the Mac /Applications/freesurfer/{7.0.0, 7.1.0, 7.1.1, …} and similarly on linux under /usr/local/freesurfer/{version}. If you have an older 5.X or 6.X version of freesurfer  installed “generically” as /Applications/freesurfer (or /usr/local/freesurfer on linux) then I recommend moving it to live under a child subdirectory with a version number as Andrew listed below.  This will allow the installers to maintain different versions of freesurfer for forthcoming releases. - R. On May 25, 2021, at 22:29, Boa Sorte Silva, Narlon <narlon.silva(a)ubc.ca> wrote:        External Email - Use Caution        Thanks for the quick reply Andrew!Nárlon CássioNárlon Cássio Boa Sorte Silva PhD (He, Him, His)CIHR and MSFHR/PARF Postdoctoral Research FellowAging, Mobility, and Cognitive Health LabDjavad Mowafaghian Centre for Brain HealthDepartment of Physical Therapy, Faculty of MedicineUniversity of British ColumbiaVancouver, CanadaTwitter: @BoaNarlonOn May 25, 2021, at 5:04 PM, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote:[CAUTION: Non-UBC Email]Hi Nárlon, There’s no harm in installing multiple versions of freesurfer on one filesystem. The FS distribution is confined to the directory it’s installed to, so we suggest organizing a FREESURFER_HOME directory structure like: /Applications/freesurfer/5.3/Applications/freesurfer/6.0/Applications/freesurfer/7.1.1 etc… when installing different distributions. Just make to correctly source the directories when using different versions. Best,Andrew From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Boa Sorte Silva, Narlon <narlon.silva@ubc.ca>Date: Tuesday, May 25, 2021 at 6:17 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh..harvard.edu>Subject: [Freesurfer] Multiple Versions Installed        External Email - Use Caution        Dear FreeSurfer experts,  I was wondering if there are any problems in having installed two different versions of FreeSurfer on the same MacOS computer? We have 5.3 installed and wanted to install 7.1.1, but keep the older version in case older data processed in the 5.3 needed to be reanalyzed. Would we run into any problems by installing the new version and processing new data with it? Thanks,Nárlon CássioNárlon Cássio Boa Sorte Silva PhD (He, Him, His)CIHR and MSFHR/PARF Postdoctoral Research FellowAging, Mobility, and Cognitive Health LabDjavad Mowafaghian Centre for Brain HealthDepartment of Physical Therapy, Faculty of MedicineUniversity of British ColumbiaVancouver, CanadaTwitter: @BoaNarlon _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1F3KLQq7oCoCP4f8lPjjLAWXQFYhntflyV9X9L… 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/1OrPdBPlz4twB1GOAGDbbzcNHQoGvoa1WPfNbCQ…;. 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Multiple Versions Installed
by Boa Sorte Silva, Narlon 25 May '21

25 May '21

External Email - Use Caution Dear FreeSurfer experts, I was wondering if there are any problems in having installed two different versions of FreeSurfer on the same MacOS computer? We have 5.3 installed and wanted to install 7.1.1, but keep the older version in case older data processed in the 5.3 needed to be reanalyzed. Would we run into any problems by installing the new version and processing new data with it? Thanks, Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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Matlab R2014b exits while executing segmentThalamicNuclei.sh in FS v7.1.1 under OS Big Sur
by Xin Qiao 25 May '21

25 May '21

External Email - Use Caution As mentioned, recon-all function with T1 MRI data works well with no problem at all. With results from recon-all, while trying to run segmentThalamicNuclei.sh, MATLAB quit with message as follows: ------------------------------------------------------------------------ Segmentation violation detected at Wed May 19 19:42:08 2021------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/7.1.1/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 69 Stepping 1, GenuineIntel Software OpenGL : 0 Virtual Machine : Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Quartz Fault Count: 1 Abnormal termination:Segmentation violation Register State (from fault): RAX = 0000000000000000 RBX = 0000000000000000 RCX = 0000000000000000 RDX = 0000000000000000 RSP = 0000000000000000 RBP = 0000000000000000 RSI = 0000000000000000 RDI = 0000000000000000 R8 = 0000000000000000 R9 = 0000000000000000 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00007000029b8d00 R13 = 00007fff2041d4bd R14 = 00007fff87147cf8 R15 = 00007000029b8da0 RIP = 0000000000003002 RFL = 00007fa5bda93250 CS = 0000000000000000 FS = 0000000000000000 GS = 000000010f288560 Stack Trace (from fault):[ 0] 0x000000010eedce64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052[ 1] 0x000000010eee0a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906[ 2] 0x000000010eee0477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119[ 3] 0x0000000117c5fb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146[ 4] 0x0000000117c5fe58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880[ 5] 0x0000000117c5d733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275[ 6] 0x00007fff2049dd7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029[ 7] 0x0000000000000000 <unknown-module>+00000000[ 8] 0x000000010df9a6ca /Applications/freesurfer/7.1.1/lib/gcc/lib/libstdc++.6.dylib+00063178 _ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+00000186 This crash report has been saved to disk as /Users/transmri/matlab_crash_dump.9882-1 ** Caught "std::exception" Exception message is:FatalException ------------------------------------------------------------------------ std::terminate() detected at Wed May 19 19:42:10 2021------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/7.1.1/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 69 Stepping 1, GenuineIntel Software OpenGL : 0 Virtual Machine : Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Quartz Fault Count: 2 Abnormal termination:Segmentation violation Register State (from fault): RAX = 0000000000000000 RBX = 0000000000000000 RCX = 0000000000000000 RDX = 0000000000000000 RSP = 0000000000000000 RBP = 0000000000000000 RSI = 0000000000000000 RDI = 0000000000000000 R8 = 0000000000000000 R9 = 0000000000000000 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00007000029b8d00 R13 = 00007fff2041d4bd R14 = 00007fff87147cf8 R15 = 00007000029b8da0 RIP = 0000000000003002 RFL = 00007fa5bda93250 CS = 0000000000000000 FS = 0000000000000000 GS = 000000010f288560 Stack Trace (from fault):[ 0] 0x000000010eedce64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052[ 1] 0x000000010eee0a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906[ 2] 0x000000010eee0477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119[ 3] 0x0000000117c5fb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146[ 4] 0x0000000117c5fe58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880[ 5] 0x0000000117c5d733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275[ 6] 0x00007fff2049dd7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029[ 7] 0x0000000000000000 <unknown-module>+00000000[ 8] 0x000000010df9a6ca /Applications/freesurfer/7.1.1/lib/gcc/lib/libstdc++.6.dylib+00063178 _ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+00000186 Abnormal termination:std::terminate() Register State (captured): RAX = 0000000000000000 RBX = 00007000029be578 RCX = 0000000000000000 RDX = 0000000000000000 RSP = 00007000029bde10 RBP = 00007000029be130 RSI = 0000000000000000 RDI = 0000000000000000 R8 = 0000000000000000 R9 = 0000000000000000 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00007000029bed00 R13 = 0000000000000000 R14 = 00007fff80752070 R15 = 0000000000000000 RIP = 000000010eee1e8b RFL = 0000000000000000 CS = 0000000100000001 FS = fffffffffffffff8 GS = 0000000000000000 Stack Trace (captured):[ 0] 0x000000010eedce64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052[ 1] 0x000000010eee0a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906[ 2] 0x000000010eee0477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119[ 3] 0x0000000117c5fb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146[ 4] 0x0000000117c5fe58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880[ 5] 0x0000000117c5f3a0 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00385952 _Z32mnRunPathDependentInitializationv+00001136[ 6] 0x0000000117c5ee54 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00384596 _Z22mnInstallCrashHandlersv+00000420[ 7] 0x000000010df98698 /Applications/freesurfer/7.1.1/lib/gcc/lib/libstdc++.6.dylib+00054936 _ZN10__cxxabiv111__terminateEPFvvE+00000008[ 8] 0x000000011890b7f1 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945[ 9] 0x000000010e335005 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205[ 10] 0x00000001193c8a65 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501[ 11] 0x000000010e404a45 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693[ 12] 0x000000010e400152 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834[ 13] 0x000000010e3ffe5e /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078[ 14] 0x0000000117c1e18f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095[ 15] 0x0000000117c1e49f /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335[ 16] 0x0000000117c04d1b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059[ 17] 0x00007fff20458954 /usr/lib/system/libsystem_pthread.dylib+00026964 _pthread_start+00000224[ 18] 0x00007fff204544a7 /usr/lib/system/libsystem_pthread.dylib+00009383 thread_start+00000015 This crash report has been saved to disk as /Users/transmri/matlab_crash_dump.9882-2 ** MATLAB is exiting because of fatal error/Applications/freesurfer/7.1.1/bin/run_SegmentThalamicNuclei.sh: line 33: 9882 Killed: 9 /Applications/freesurfer/7.1.1/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei Test001 /Applications/freesurfer/7.1.1/subjects/2108220/ 0.5 /Applications/freesurfer/7.1.1/average/ThalamicNuclei/atlas/AtlasMesh.gz /Applications/freesurfer/7.1.1/average/ThalamicNuclei/atlas/AtlasDump.mgz /Applications/freesurfer/7.1.1/average/ThalamicNuclei/atlas/compressionLookupTable.txt 0.05 L-BFGS v12 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr /Applications/freesurfer/7.1.1/bin/' 1 0Darwin TransMRIs-Mac-mini.local 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 Many thanks in advance for any solution or hint! Joe

2 2

Recon-all error
by g.toniol＠libero.it 25 May '21

25 May '21

External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I am new to Freesurfer and I apologize if my question is naive but I cannot find a solution in any of the online resources. I successfully set up Freesurfer and I am now attempting to run recon-all on a .nii file ("s44891-153636-00001-00192-1.nii") on a MacOs Big Sur. To do so, I run the command below, where "S001" is the subject name and "/Users/giorgio/Documents/MATLAB/spm12/Group 0/S001/scans/struct/s44891-153636-00001-00192-1.nii " is the path to the .nii image file: ..$ recon-all -s S001 -i /Users/giorgio/Documents/MATLAB/spm12/Group 0/S001/scans/struct/s44891-153636-00001-00192-1.nii -all However, I get the following error: "ERROR: You cannot give recon-all a folder as input. It must be an image file. If you have multiple files, you need multiple -i flags. Darwin macbook-pro.home 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 recon-all -s S001 exited with ERRORS at Mon May 24 15:50:32 CEST 2021" My input volume is a .nii, an image file, and I copied its pathway automatically so I do not think there are mistakes in the pathway to the image: do you see why is it considered as a folder? Can you help me troubleshoot? Thank you! Best, Giorgio PS I have already tried to restart the program, to change directory on terminal, to convert manually the files to .mgz, or to move the .nii file in the freesurfer home (which gives the following error: ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags.)

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Re: [Freesurfer] Processing MRI help
by Selvarajah, Arunan 25 May '21

25 May '21

External Email - Use Caution After subscribing to the mail list, I am re-trying this again. Best, Arunan From: "Selvarajah, Arunan" <Arunan.Selvarajah(a)uhnresearch.ca> Date: Monday, May 24, 2021 at 8:38 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Cc: Hanna Vasilevskaya <hanna.vasileuskaya(a)mail.utoronto.ca> Subject: Processing MRI help Hi, I am currently using this program to process and eventually analyze MRIs. I was able to process most of our patients, except one. It gets to the “Correcting defect” command and does not proceed any further. I waited about 24 hours before re-running the program. It still stops in the exact same spot. Below is the image of where it stops: [cidimage001.png(a)01D750DB.A767B310] What should I do? Thanks, Arunan This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization. If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following: (1) Follow any unsubscribe process the sender has included in their email (2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page. Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists. Patient Consent for Email: UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here<https://secure-web.cisco.com/1-qRtOqEpyj1C59blW0xVmKSl5xzdr2h9bzCdySuGi7dgW…> to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

2 1

FreeSurfer (v 6.0) skull stripping problems
by BDiB10 25 May '21

25 May '21

External Email - Use Caution Hi everyone, I am processing the NIFD dataset (visit 1) and the FS (v 6.0) segmentation consistently includes dura mater in the pial boundary in most subjects (I could not attach example snapshots to this email, but they are available if required). I have tried -gcut and the watershed algorithms for FS and they do not seem to be making a difference. Considering that the default preflooding height in FS is 25, I chose 20 and 1 for additional processing. While PFH=1 (and -gcut) does not remove the skull left behind (just shaves off some boundary pixels), using PFH=20 (oddly) seems to actually add more pixels. These observations are based on the brainmask.mgz output after running “ recon-all -skullstrip -wsthresh <pf height> -clean-bm -subjid <subid>” and “recon-all -skullstrip -clean-bm -gcut -subjid <subjid>” (and without fully reprocessing the data). - I would be very grateful for any insights about additional methods to try to remediate this problem, short of manual editing. This is a widely occurring issue in the dataset, so we cannot just exclude the problem cases. - Would it be advisable to use different software for the skull stripping (such as BET) and use that output in the FS pipeline? - Could I be missing something (this is the first time I am using FS)? Thank you very much for your time! Best regards, Divya

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