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Advanced fMRI Applications Postdoctoral Fellow Position at Carle Health
by Yendiki, Anastasia 17 Mar '22

17 Mar '22

Passing along this opening at the Carle Illinois Advanced Imaging Center on behalf of Dr. Sheeba Arnold Anteraper: https://www.ismrm.org/jobs/j07799.pdf Anastasia.

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Trac-all -prep -c error
by Kaplan, Elizabeth 17 Mar '22

17 Mar '22

External Email - Use Caution Hello All, I am attempting to process images using tracula, however I am running into an error when attempting to run the "trac-all -prep -c" command line. Parcellation was ran on FS 7.2.0, However, I am running the command on freesurfer dev version due to an earlier resolved error reading index file: https://secure-web.cisco.com/1NrhFqWiJIFbTxyFpNb7jAq78TXhI1EKDKQf_a4RRwqAAO… Trac-all exits on the command: CMD mri_binarize --i /autofs/cluster/lazar/Projects/DTIanalysis/Subjects_DTI_t1t2/AG010_1308_T1_LAZAR_recon.long.AG010_1308/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /autofs/cluster/lazar/Projects/DTIanalysis/Subjects_DTI_t1t2/AG010_1308_T1_LAZAR_recon.long.AG010_1308/dlabel/anatorig/aparc+aseg_mask.nii.gz The Trac-all.log reads "mri_binarize done", see attached, and the outputs from the mri_binarize command are present. I used the longitudinal configuration file example on the wiki, attached below. Any guidance on how to navigate the issue would be greatly appreciated! Thank you!

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Re: [Freesurfer] Reposting TRACULA trac-all -prep finishes with errors
by Goeckner, Bryna 17 Mar '22

17 Mar '22

External Email - Use Caution Attaching config file & link to trac-all.log (trac-all/log is kind of big – so freesurfer listserv blocked email). Hopefully you are able to access them this way. https://secure-web.cisco.com/12mEXYhuUBlTXDgjHzPTswpMwBUz25h_vFGE_6-rakbDLz… From: Goeckner, Bryna <bgoeckner(a)mcw.edu> Date: Monday, February 14, 2022 at 4:42 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: TRACULA trac-all -prep finishes with errors Hi FreeSurfer Developers, I am attempting to run data for several subjects through TRACULA using trac-all -prep, but some of them have finished with errors. I have checked registration for all of them and it looks ok. I am including a link to my config file, and the trac-all.log and trac-all.error files for one subject: https://secure-web.cisco.com/12G4PlLvcpklUuTh8D_a28ezMniUQvE-KhDPzm3bm138_O… FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b Any help you can give me is greatly appreciated. Thanks! Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program

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error with trac-all -prep in FS7.2 tracula
by Alexopoulos, Dimitrios 17 Mar '22

17 Mar '22

External Email - Use Caution Hi all, We are reprocessing some of our data with FS 7.2 to evaluate the new updates to Tracula, however, we are getting errors from the trac-all -prep -c configfile step. The last 20 lines of output are shown below. Anyone have any comments on how to correct this? ------------------------------------- trac-preproc exited with ERRORS at Fri Feb 11 18:18:29 CST 2022lines: 1DIAGNOSTIC, 24, -4.743908838687e-01, 5.860622007851e-05, 4.2190e+01, 1.4997e+00, 1DIAGNOSTIC, 25, -4.743823138430e-01, 4.831431802083e-05, 4.3721e+01, 1.5312e+00, 1DIAGNOSTIC, 26, -4.744830990496e-01, 3.946018283887e-05, 4.5293e+01, 1.5718e+00, 1DIAGNOSTIC, 27, -4.744857576549e-01, 3.343839305766e-05, 4.6879e+01, 1.5857e+00, 1DIAGNOSTIC, 28, -4.744568952592e-01, 2.896457797682e-05, 4.8446e+01, 1.5669e+00, 1DIAGNOSTIC, 29, -4.744930355970e-01, 2.351784987169e-05, 5.0045e+01, 1.5996e+00, 1DIAGNOSTIC, 30, -4.744428763349e-01, 1.764564796251e-05, 5.1621e+01, 1.5762e+00, 1DIAGNOSTIC, 31, -4.744390742695e-01, 1.211632175497e-05, 5.3234e+01, 1.6130e+00, 1DIAGNOSTIC, 32, -4.744465209349e-01, 6.742111363235e-06, 5.4833e+01, 1.5989e+00, 1DIAGNOSTIC, 33, -4.743750058790e-01, 8.816157837238e-07, 5.6420e+01, 1.5867e+00, Elapsed time (stage 2): 58.59 Total elapsed time: 71.08 ConvertTransformFile 3 /data/shimony/shimony2/neonatal/wunder_9_10yo/freesurfer7.2/neo289e/dmri/xfms/diff2syn0GenericAffine.mat /data/shimony/shimony2/neonatal/wunder_9_10yo/freesurfer7.2/neo289e/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux hopper 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux That piece of code is part of the ANTS library. When I look at the code this is what I see (or don't see for that matter) # Register FA nonlinearly to FA template with SyN set cmd = $ANTSPATH/antsRegistrationSyNQuick.sh <-- This ANTs code has $ANTSPATH set cmd = ($cmd -d 3) set cmd = ($cmd -m $dwidir/dtifit_FA.nii.gz) set cmd = ($cmd -f $intertrg) set cmd = ($cmd -o $xfmdir/diff2syn) echo $cmd |& tee -a $LF |& tee -a $CF if ($RunIt) then $cmd |& tee -a $LF if ($status) goto error_exit endif # Convert affine transform to .lta set cmd = ConvertTransformFile <-- This ANTs code DOES NOT have $ANTSPATH ________________________________ 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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TRACULA trac-all -prep finishes with errors
by Goeckner, Bryna 17 Mar '22

17 Mar '22

External Email - Use Caution Hi FreeSurfer Developers, I am attempting to run data for several subjects through TRACULA using trac-all -prep, but some of them have finished with errors. I have checked registration for all of them and it looks ok. I am including a link to my config file, and the trac-all.log and trac-all.error files for one subject: https://secure-web.cisco.com/1fMOW2H4XkhFM0lHgtKrt25eEfHZNAPKOFCoBf2ppUW5T2… FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b Any help you can give me is greatly appreciated. Thanks! Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program

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how to load flat surface in freeview
by Francesca Strappini 17 Mar '22

17 Mar '22

External Email - Use Caution Dear Freesurfer experts, I'm trying to load the flat surface that I created with this command line: mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d I tried loading the patch inside freeview but I got this error message: [francesca@GIOVE surf]$ tksurferfv sub01_mprage lh inflated freeview -f /home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.inflated:curvature=/home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.curv -viewport 3d ASSERTION FAILED: /home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 mris->dist_nsize == 0 ASSERTION FAILED: /home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 mris->dist_nsize == 0 Errore di accesso al segmento di memoria (creato file core) And I tried to run this command line but nothing happened: [francesca@GIOVE surf]$freeview -f lh.inflated:patch=lh.full.flat.patch.3d Thank you, Francesca -- Francesca Strappini, Ph.D. Psychology Department Sapienza University of Rome Via dei Marsi 78, Rome 00185 Italy Tel.: +39 392 151 4029 E-mail: francesca.strappini(a)uniroma1.it <francescastrappini.stud(a)uniroma1.it>

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Re: [Freesurfer] bug: freeview's "configure overlay" window frozen (Ubuntu18 in wsl2 on Windows 11)
by Sebastien Proulx 16 Mar '22

16 Mar '22

External Email - Use Caution Thanks for the tip Ruopeng! Just tried MobaXterm. Nice piece of software! I had to enable hardware acceleration (mobaXterm -> settings -> X11 -> OpenGL acceleration -> Hardware) for freeview to work at all, but it worked-now the configure overlay window does not freeze. Two draw backs though: -Rendering behaves weirdly. Every now and then (within few seconds), while just moving the mouse, the brain just disappears, and only reappears when I rotate it by click-and-drag. It does not prevent one to get something done, but it is frequent enough to be quite disturbing :-( -Graphics seem to only go through the (moba)Xserver when the wsl is launched from within mobaXterm. When launching wsl through other means (e.g. command prompt), freeview does open but the window outline looks different and the initial problem is back, as if graphics go through another Xserver... (and by the way, I completely removed Xming !) I am generally confused with Xserver stuff, but does the last point suggest that wsl in Windows 11 (build 22000) has its own Xserver-like capability? Would make sense with Windows upping its game for the integration wsl graphics into the windows desktop (https://secure-web.cisco.com/1WiSJsgR_rkzEwjyT1ydiRFw_EKqkfi02STKKjfu1AoEsO…) Any more advice on either (1) getting moba render to work more smoothly, (2) having wsl actually use Xming or (3) having freeview and native wsl graphics live happily together? Thanks a lot for the help and Good night! Sébastien

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Atlas of primary motor and auditory cortex
by Jingyi Wang 16 Mar '22

16 Mar '22

External Email - Use Caution Hello Freesurfer experts, I ran the recon-all command and got all the .label files for the segmentations of the cortical areas. However, I have some questions about the label for primary motor and auditory cortex. - I found two types of labels associated with the primary motor cortex: lh.L_M1.label and lh.BA4a_exvivo.label. Are they both valid, and the lh.BA4a_exvivo.label segmentations are finer parcellation than the other one? - What's the primary auditory cortex .label file? Thanks in advance! ________________________ Jingyi Wang Postdoctoral Scholar LEAP Neuro Lab Psychological & Brain Sciences University of California, Santa Barbara

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complete unfinished steps of recon all
by Hossein Rahimzadeh 16 Mar '22

16 Mar '22

External Email - Use Caution Hello FreeSurfer Developers, Due to the fact that the freesurfer runs for a long time, the computer is turned off several times during the run due to electricity fluctuations. How to complete unfinished steps of recon-all. I tried to continue the analysis with the command "recon-all -make all -s subject, but" I got the following error: ERROR: -make is no longer supported 1)freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2)linux ubuntu 20.04 3)two recon-all.log of two subjects have attached Best regards, Hossein Rahimzadeh Biomedical Engineering, MSc. Shahid Beheshti University of Medical Sciences, Tehran, Iran.

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bug: freeview's "configure overlay" window frozen (Ubuntu18 in wsl2 on Windows 11)
by Sebastien Proulx 16 Mar '22

16 Mar '22

External Email - Use Caution Dear Freesurfers, I just installed Freesurfer (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) on Ubuntu (Ubuntu 18.04.6 LTS) running in Windows 11's wsl2. So far Freeview is running fine-I can load volumes and surfaces, and add an overlay to a surface-but configuring an overlay fails: the "configure overlay" window freezes at opening and even the x button to close the window does not work. No error message on the command terminal. Is this a known bug? Any fix or workaround? Thanks and Have a very good day! Sébastien

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