Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

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

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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.

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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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Fwd: confirm 8038f95159942b876b5e8f8110930301c8222d61
by Andrew Raines 24 May '21

24 May '21

External Email - Use Caution Hi there, I really need some help…I have experienced a mild/moderate head injury in 1997 which caused me to go into seizures (no family history of epilepsy) I have had MRI recently done as my cognitive function and memory have declined rapidly over the years, after the accident I apparently changed from very happy and a large group of friends to being grumpy and short with people and making inappropriate comments... i also lost all my friends at the time as my mood changed and i have struggled to retain friendships (even new ones) since the accident. I have tried to follow your instructions of how to install free surfer but despite once being proficient on c basic programming I have been unable to follow instruction on how to install run and process my MRI data. I was hoping that you may have an angel that would be able to uplift my MRI data from dropbox, process and send it back to me, in lou of being able to use my MRI for any research, the neurologist only look at the MRI data with the naked eye and say i look normal…im hoping that freesurfer will show evidence otherwise so that the government based accident coverage can get me sent to australia for analysis as there is no way the hundreds of falls and head injury i have had can leave me “normal” yet barely functional thank you for any help you may be able to give Kind Regards Andrew Raines > Begin forwarded message: > > From: Andrew Raines <andrewraines(a)me.com> > Subject: Re: confirm 8038f95159942b876b5e8f8110930301c8222d61 > Date: 25 May 2021 at 11:04:46 AM NZST > To: freesurfer-request(a)nmr.mgh.harvard.edu > > > >> On 25/05/2021, at 11:03 AM, freesurfer-request(a)nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: >> >> confirm 8038f95159942b876b5e8f8110930301c8222d61 >

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Thalamus/hippocampus subfield question
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 24 May '21

24 May '21

?Hi, I am visually quality checking the hippocampal and the thalamic subnuclei parcellations that Iglesias designed. I see that the hippocampal tail and the PuM (pulvinar) overlay with each other. What should I make of that? Is that a brain worth removing from analysis? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Job opportunity (ResearchAssistant/Lab Manager) at Boys Town National Research Hospital
by Sahil Bajaj 21 May '21

21 May '21

External Email - Use Caution *Business:* Boys Town National Research Hospital *Job Summary:* As a Research Assistant/Lab Manager of the Center for Neurobehavioral Research (CNR), you join us in our work understanding the neurobiological bases of adolescent externalizing and internalizing conditions. In this role, you will be an integral member of the scientific team and will have rich opportunities to participate in and learn from the Neurobehavioral Development Study and multiple other neurodevelopmental studies from across the CNR. The CNR and Boys Town National Research Hospital provide an ideal training environment for research assistants with extensive opportunities to learn about clinical practice and fMRI. Review of applications will begin as soon as they are received and will continue until the position is filled. Anticipated start date is July to August 2021. *Schedule*: Full-Time, 40 hours a week *Responsibilities:* - Ensures that all laboratory materials, supplies, and equipment are ordered and available. - Performs or assists in the recruitment of research participants, including patients. Collaborates with laboratory PI to understand their recruiting needs. - Performs or assists in testing of research subjects. - Maintains detailed records of test conditions and results. - Manages purchasing of equipment and financial details (e.g. subject payment, petty cash, and mileage reimbursements). - Regularly enters data into lab databases and ensures scoring and data accuracy. *Required Qualifications:* - Requires a BSc/BA degree directly related to the work involved in the research program (i.e., Psychology or Neuroscience). - Experience in Mental Health or other forms of psychological research, preferred - Job requires interpersonal skills, close attention to detail, and flexibility in duties performed. About us: The Center for Neurobehavioral Research was established in 2016 to help improve the care of children through a better understanding of the neurobiology of mental health. With a new, dedicated and state-of-the-art 3 Tesla scanner as well as fNIRS capability, the CNR assesses approximately 300 adolescents and a comparable number of young children annually on a large neuroimaging battery, including tasks indexing emotion processing, decision-making and response control, to determine dysfunction in specific neuro-cognitive systems that underpin different forms of impaired mental health. In addition to in-home family services and residential treatment centers, Boys Town provides the Family Home ProgramSM, a treatment foster-case program serving over 400 youth annually on the Boys Town campus in Omaha, Nebraska. Youth participating in the Family Home ProgramSM are scanned before and after treatment completion to determine treatment response. The CNR is also involved in the assessments of other interventions – both pharmacological and psychosocial. The CNR therefore offers a unique opportunity to study mechanisms underlying mental health issues in large samples, with a translational focus. The CNR provides a vigorous and highly collaborative research environment in which post-doctoral fellows participate in team-based projects. *For any questions/queries, please contact:* *Sahil Bajaj, PhD* Director Multimodal Clinical Neuroimaging Laboratory (MCNL) E-mail: sahil.bajaj(a)boystown.org *&* *James Blair, PhD* Director, Center for Neurobehavioral Research E-mail: james.blair(a)boystown.org *About Boys Town:* Boys Town has been changing the way America cares for children and families since 1917. With over a century of service, our employees have helped us grow from a small boarding house in downtown Omaha, Nebraska, into one of the largest national child and family care organizations in the country. With the addition of Boys Town National Research Hospital in 1977, our services branched out into the health care and research fields, offering even more career opportunities to those looking to make a real difference. Our employees are our #1 supporters when it comes to achieving Boys Town's mission, which is why we are proud of their commitment to making the world a better place for children, families, patients, and communities. Unique perks to Boys Town employees and their families include free visits to Boys Town physicians and free prescriptions under the Boys Town Medical Plan, tuition assistance, parenting resources from our experts and professional development opportunities within the organization, just to name a few. Working at Boys Town is more than just a job, it is a way of life. *Boys Town National Research Hospital is a tobacco free campus. * *This advertisement describes the general nature of work to be performed and does not include an exhaustive list of all duties, skills, or abilities required. Boys Town is an equal employment opportunity employer and participates in the E-Verify program. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability or veteran status. To request a disability-related accommodation in the application process, contact us at 1-877-639-6003.* -- ------------------------------------- *Sahil** Bajaj, Ph.D.* Director, Multimodal Clinical Neuroimaging Laboratory (MCNL) Center for Neurobehavioral Research sahil.neurores(a)gmail.com <sahil.neuro(a)gmail.com> | *p:* 531.355.1053 | *f:* 531.355.1213 Boys Town National *ResearchHospital* Boys Town, NE 68010 Twitter <https://secure-web.cisco.com/1GhmQmh4D8P6bUJ0iA6LJTAMyO9fslBVipNwyODy2iO0hz…> | LinkedIn <https://secure-web.cisco.com/1MbBJOYkdkPSNlqZd9IFIr7yku1XwF8sFCDJsw_2p3tjAb…>

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