Freesurfer

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30070 discussions

Talairach failed error
by Romeo Penheiro 11 Sep '22

11 Sep '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute the FreeSurfer outputs for one of my subjects. I get the following error when I run the recon-all command: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0077, pval=0.0000 < threshold=0.0050) I've searched the list and one similar error has been reported<https://secure-web.cisco.com/1mb7ICnEk6d7MX8y2VUywYPvb7bDBqwKBiUBJRRl0MYz9P…> in fMRIPrep. However, I am not sure how to implement this on the platform. Does anyone have any thoughts on how to troubleshoot this one? Also, I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: v7.2.0 2) Platform: CBRAIN 3) uname -a: Linux cdr854.int.cedar.computecanada.ca<http://secure-web.cisco.com/1S0ZPkqWcDQh46lUo_Qq5ag8EA7S14eBo9cHG1xCnN5nATS…> 3.10.0-1160.53.1.el7.x86_64 #1 SMP Fri Jan 14 13:59:45 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Romeo Penheiro Master's Student - Cognitive Science Program Carleton University This email contains links to content or websites. Always be cautious when opening external links or attachments. Please visit https://secure-web.cisco.com/1PY_amCYECNNWCwzy3R4JIwB68nuCzqGc5BQ-T7BjvfW8o… for information on reporting phishing messages. When in doubt, the ITS Service Desk can provide assistance. https://secure-web.cisco.com/1RwAwHBYZhklMOEk6WUWXJsqLCukS6Gr7jS6yOEgcPy-3n… -----End of Disclaimer-----

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Re: [Freesurfer] problem with autorecon2-cp
by Mostafa Fakhri 10 Sep '22

10 Sep '22

External Email - Use Caution Thank you for sharing your expertise. Mostafa

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ls: *.nii: No such file or directory
by Ellie Shaw 09 Sep '22

09 Sep '22

External Email - Use Caution i there, I am attempting to perform the recon-all in parallel command. When I run this command I get the following message: ls: *.nii: No such file or directory The following command is: bash-3.2$ export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/tbi/TBN bash-3.2$ echo $SUBJECTS_DIR /Applications/freesurfer/7.2.0/tbi/TBN bash-3.2$ ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache ls: *.nii: No such file or directory Academic tradition requires you to cite works you base your article on. If you use programs that use GNU Parallel to process data for an article in a scientific publication, please cite: Tange, O. (2022, August 22). GNU Parallel 20220822 ('Rushdie'). Zenodo. https://secure-web.cisco.com/1mGw517t0yBXkztNqf01JZCPURoO6_GwJZcmOf9XN0Bit3… This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing. More about funding GNU Parallel and the citation notice: https://secure-web.cisco.com/1qeJBgbE0rR_XWDJGaS_dtrryFt6t984jQGxAubuxxJ-dk… To silence this citation notice: run 'parallel --citation' once. I have also attached a screenshot of the file with the nii files to help. I am seeking some support to overcome this issue. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b Platform: OSX 7.2.0 Thank you in advance! Kind regards, Ellie

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equest for password to open FS_7_2_0_Ubuntu_18_04_06.ova.7z, reg:-
by PRASAD D 09 Sep '22

09 Sep '22

External Email - Use Caution Dear sir/madam. My name is D.Prasad from PTU university, Puducherry, INDIA. I'm a research scholar at PTU university. my research area deals with Brain MRI Images. to work on that, i have downloaded (Ubuntu 18.04.06 compressed image with the *FreeSurfer <https://secure-web.cisco.com/1QXoCtx-MIiYDhd3WUA3RA2DLeZHX5T78Sq0bvhIq3vqTy…> 7.2.0 release installed)* FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/10p_AiCmfuT7rYhn0VynvFaHc0KgMJaRONhMsmtslzUKju…> When I'm trying to open the above file, it is asking for Password. I kindly request you to send the Password at the earliest. Thank you Yours Sincerely D.Prasad Fulltime Research Scholar

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Problems Freesurfer 5.3 License on Ubuntu 20
by Ludwig, Rüdiger 09 Sep '22

09 Sep '22

Hello, We have a problem with our license for Freesurfer 5.3 on Ubuntu 20. Previously we used the same license on our old computing node on CentOS 7 without any problems. On our new node we get this message: ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer/5.3/license.txt We tried it with the old license and even requested a new one. Both produce the same error. Thank you in advance for any hints on how to solve this Best regards, Rüdiger --- Rüdiger Ludwig (he/him) IT-Service European Neuroscience Institute A Joint Initiative of the University Medical Center Göttingen and the Max Planck Society Grisebachstr. 5 37077 Göttingen Tel: +49 551-39 61308 Email: <mailto:r.ludwig@eni-g.de> r.ludwig(a)eni-g.de Office: <https://secure-web.cisco.com/17_o9SArx5GL4f8cePQRv4LgkQlr_EYJPu2W_VeWEEZdq_…> 0.051 External Email - Use Caution

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SNR
by Marina Fernández 08 Sep '22

08 Sep '22

External Email - Use Caution Dear experts, I would like to calculate the SNR by dividing the mean intensity of the signal of interest by the SD of the noise. To do this, I would like to create a small circular ROI and place it within the region of interest and a larger circular ROI and place it within the 'background' region that is parcelled to each subject in apas+head.mgz (ID=130). Do you know what functions I can use to create these ROIs and place them within the regions I want? Do you know a better method to calculate the SNR? Thank you in advance. Best regards, Marina

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Vanderbilt University HBCD postdoc opportunity
by Harriott, Emily M 08 Sep '22

08 Sep '22

External Email - Use Caution Dear FreeSurfer subscribers, The HBCD site at Vanderbilt University (Nashville, TN) is taking applications for a postdoctoral fellow in developmental neuroscience. Please see the below posting. Feel free to forward to anyone you know who might be interested. Thank you, Emily Applications are invited for a postdoctoral fellowship in developmental neuroscience at Vanderbilt University’s Peabody College of Education. Individuals will be mentored by Laurie Cutting and an interdisciplinary mentorship team formed from Vanderbilt investigators studying the neuroscience of child development (the Healthy Brain and Cognitive Development (HBCD) study, a national study recruiting women during pregnancy and following their infants through the first five years of their lives. https://secure-web.cisco.com/1CNKEuoH7g6UlSY_LHBmbreriRfxoDPh3Hd-lhVTIPBK1c…) Composition of the mentor team will be tailored to the individual’s interests; possible members include Kate Humphreys, Autumn Kujawa, Sarah Osmundson, Sasha Key, Seth Smith, and Bennett Landman. Individuals will have the opportunity to work on several large NIH-funded projects, including the HBCD study, as well as other longitudinal neuroimaging studies focused on academic, cognitive, behavioral outcomes in early childhood development (starting at perinatal period) through elementary school. Research opportunities will include analysis and writing manuscripts using already collected multimodal MRI datasets, travel and conference presentations, and support for writing mentored grant proposals. Ideal candidates should be highly motivated to publish first-author papers and present at conferences, and should possess a background in advanced statistics, strong experimental and scientific writing skills, ability to work in a team environment, and be self-motivated. Experience working with children in a research setting is also desired. Additional desired strengths include competence in MRI and/or EEG data acquisition/analysis and/or assessment training, including programming skills (e.g., Matlab, R, and/or Python) and experience with multimodal neuroimaging (DWI, fMRI, and/or EEG) analysis. If you are interested in the position, please email Laurie Cutting (Laurie.Cutting(a)Vanderbilt.Edu<mailto:Laurie.Cutting@Vanderbilt.Edu>) a recent CV, a brief statement of research interests (1 page), and the contact information for 2 references. Applications will be considered on a rolling basis until position(s) are filled. Salary is highly competitive and reimbursement for moving expenses will be considered.

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Enabling AVX instructions on Windows 10 (was Re: Illegal Instruction (mri_segment_hypothalamic_subunits) - VM 7.2.0
by fsbuild 08 Sep '22

08 Sep '22

External Email - Use Caution The lscpu output in the VM not listing AVX and AVX2 does not necessarily mean something is missing from the VM to run AVX instructions. The Intel processor listed in your output, i7-8700K, does support AVX instructions.  But AVX instructions could be disabled on your host (windows) machine preventing the VM from running them.  Microsoft's own virtualization or “hyper-v” software may also be interfering with Virtualbox. If you start the VM and open the terminal window you should see the output from the freesurfer startup script list SUBJECTS_DIR, etc.  You can run the included python distribution by typing “fspython” .  At the next prompt, type “import tensorflow”.   I think you will get an illegal instruction error and a core dump when you do that since the VM cannot currently run AVX instructions. developer#developer-VirtualBox:~$ fspython Python 3.6.8 (default, Apr 10 2020, 02:08:58) [GCC 4.4.7 20120313 (Red Hat 4.4.7-23)] on linux Type “help”, “copyright”, “credits” or “license” for more information. >>> import tensorflow … Illegal instruction … (core dumped) ... This post describes what I think you are seeing on a Windows machine hosting an Ubuntu VM, https://secure-web.cisco.com/19O5GzeIOczV4HAYp0Qnt_9uKmjbtCZBRgyUgeds9Wu7V_… … and this lists how to enable/disable AVX instructions … https://secure-web.cisco.com/16x1EXOU9g3xPZwbDofNjDwkp8aKV6kSl8PPbTnOAXFsM8… From those and other posts I would try the following on your Windows (host) machine: 1) Open the windows terminal or command line window in administrator mode 2) Enable AVX instructions with the command    BCDEDIT /set xsavedisable 0 3) Disable launching the Microsoft hypervisor    BCDEDIT /set hypervisorlaunchtype off 4) Shut down the VM and quit Virtualbox.  You may want to quit all other applications as this next command may ask to reboot your machine (say yes).  If you are not prompted to reboot, then manually reboot the Windows host. 5) Disable Microsoft Hyper-V    DISM /Online /Disable-Feature:Microsoft-Hyper-V 6) After your machine reboots, login and start the VM 7) In the VM Ubuntu terminal window, run “lscpu | grep avx” again and see if it lists avx, avx2 8) IF IT DOES REPORT AVX NOW, try the lines above again where you typed “fspython” followed by “import tensorflow”.  This time you should not get an illegal instruction error.  You can ignore any error you see about a missing library for libcuda and/or no GPU support. - R. On Sep 3, 2022, at 13:46, daedalus39(a)aol.com wrote:        External Email - Use Caution        OK.  It appears this VM (provided by the FreeSurfer developers) does not include "AVX".That is, "freesurfer_7.2.0_amd64.deb" can't run mri_segment_hypothalamic_subunits without additional setup?  Is it even possible?  If so, can anyone in the FS community provide some simple guidance.  I am not horribly facile with Linux to begin with, but I'd really like to test the hypothal function.-Randydeveloper@developer-VirtualBox:/$ lscpu | grep avxdeveloper@developer-VirtualBox:/$ lscpu | grep avx2developer@developer-VirtualBox:/$ lscpuArchitecture:        x86_64CPU op-mode(s):      32-bit, 64-bitByte Order:          Little EndianCPU(s):              4On-line CPU(s) list: 0-3Thread(s) per core:  1Core(s) per socket:  4Socket(s):           1NUMA node(s):        1Vendor ID:           GenuineIntelCPU family:          6Model:               158Model name:          Intel(R) Core(TM) i7-9700K CPU @ 3.60GHzStepping:            13CPU MHz:             3599.998BogoMIPS:            7199.99Hypervisor vendor:   KVMVirtualization type: fullL1d cache:           32KL1i cache:           32KL2 cache:            256KL3 cache:            12288KNUMA node0 CPU(s):   0-3Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni ssse3 cx16 pcid sse4_1 sse4_2 hypervisor lahf_lm invpcid_single ibrs_enhanced fsgsbase invpcid md_clear flush_l1d arch_capabilitiesdeveloper@developer-VirtualBox:/$ -----Original Message-----From: fsbuild <fsbuild(a)contbay.com>To: freesurfer(a)nmr.mgh.harvard.eduCc: daedalus39(a)aol.comSent: Fri, Sep 2, 2022 10:12 pmSubject: Re: [Freesurfer] Illegal Instruction (mri_segment_hypothalamic_subunits) - VM 7.2.0        External Email - Use Caution        Hello Randy,The mri_segment_hypothalamic_subunits command is a python script that uses tensorflow which in turn is coded to use AVX instructions.  If the VM host processor does not support AVX instructions, then you will get an illegal instruction error.You can check to see if AVX instructions are supported if this commands shows "avx" or "avx2" in the output (see screenshot for where that is the case).$ lscpu | grep avxIf AVX instructions are supported, then error can also happen if the command is incomplete.- R._______________________________________________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/1CEVAya8KDKQFfHD_Onw7klAUxX4Oo2gu4kCXH… 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 https://secure-web.cisco.com/176IszYzKAMgHnOQttsHYb9pFbTHVpmRb6Wrb3… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1FFa02IdtAC8aGqRN_pd3lLUsU2i7Gpv6wZ34l…; .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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RESOLVED: trac-all -prep ERROR printf: value not completely converted
by Wurdack, Katharina 08 Sep '22

08 Sep '22

External Email - Use Caution Hello everyone, I just wanted to share a solution to a problem I encountered when trying to run the trac-preproc script (FreeSurfer 7.3) on a machine set up outside the US. When calling xfmrot from the trac-preproc script (dorotbvecs = 1 in the configuration file due to usage of eddy_correct), I got the following error message for each of the bvec-values: printf: 'random bvec': value not completely converted If you are working outside the US, make sure that your decimal separator is set to "." and NOT ",". You can check this by entering locale decimal_point in your terminal. Changing it from "," to "." requires to change the environment variable LC_NUMERIC (see e.g. here: https://secure-web.cisco.com/13exOcfRq-44ZipqadYDq8beVNct_4LzaLbP3yLq_PxFxO…) Hopefully this can help if anyone else happens to run into the same problem! It really is just a minor issue but did cost me half a day to find my way out of it... Best, Katharina P.S.: I didn't know where/how to add this to the wiki in a meaningful way, so I decided to just post to the mail archive - hope this is okay! ---------------------------------------------------------------------------------------------- Katharina Wurdack Ärztliche und wissenschaftliche Mitarbeiterin Charité Universitätsmedizin Berlin Campus Virchow-Klinikum Klinik für Neurologie Augustenburger Platz 1 D-13353 Berlin E-Mail: katharina.wurdack(a)charite.de<mailto:deetje.iggena@charite.de> ________________________________

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FreeSurfer 7.2.0 Bug: -nuintensitycor for HighRes + sub-millimeter optimized pipeline
by Marc-Antoine Fortin 08 Sep '22

08 Sep '22

External Email - Use Caution Hi, I am currently trying the FreeSurfer 'optimized' pipeline for high-resolution (0.6mm)3 7T MPRAGE datasets as described in this link: https://secure-web.cisco.com/10HAtUm2Jw0xOwFBksoxzxFEJ8D6Vv8ds_sG8BE1pIzC3h… HighFieldRecon - Free Surfer Wiki<https://secure-web.cisco.com/10HAtUm2Jw0xOwFBksoxzxFEJ8D6Vv8ds_sG8BE1pIzC3h…> Running recon-all on data collected at 7T. See also: SubmillimeterRecon Bias correction prior to recon-all. Compared to 3T MPRAGE and MEMPRAGE scans collected at 7T have stronger intensity inhomogeneity, which won't be fully corrected in the default recon-all. surfer.nmr.mgh.harvard.edu However, I am facing issues with the inhomogeneity correction done during autorecon1. In fact, the rescaling step between orig.mgz -> orig_nu.mgz AND the '-nuintensitycorr' step between orig.mgz -> nu.mgz completely destroys the homogeneity gained from the SPM12 BiasField Correction applied beforehand. The exact command line I'm using is: $ recon-all -all -s P7T_020_001bc -hires -i BC_MPRAGE_iPat2.nii -expert expert-file.opts - where BC_MPRAGE_iPat2.nii is the output of SPM12 BiasField Correction (i.e., the bias field corrected MPRAGE image) and expert-file.opts the file containing ''mris_inflate -n 100". I am using FS version 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) on Linux Ubuntu 18.04 bionic (Linux mrphys-gpu1 4.15.0-180-generic #189-Ubuntu SMP Wed May 18 14:13:57 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux). The whole recon-all runs properly without errors, but the homogeneity is worse after the NU intensity correction... See screenshots in attachments (orig.mgz VS nu.mgz). I have also attached the recon-all.log file. I am currently testing the '-nonuintensitycor' flag, but it exited WITH errors (not the recon-all.log file attached). In addition, I tried the exact same pipeline but without passing the data through SPM12 beforehand. It still did the same thing of destroying the small amount of homogeneity in the image to an even worst level of inhomogeneity. On another matter, this part in the link I provided above is quite unclear: """ Recommended bias-correction parameters: * Bias FWHM = 18 * Sampling distance = 2 """ A Bias FWHM of 18 mm is not possible with SPM12 (minimum being 30 mm). So, is it for SPM12 or something as part of recon-all? For the sampling distance, it's fine with the 2 mm in SPM12. Have a great day! 🙂 Marc-Antoine _______________________________ Marc-Antoine Fortin +47 45 84 99 61 Stipendiat / PhD Candidate Department of Physics Norwegian University of Science and Technology (NTNU) [cid:95742765-3552-411c-86af-f0811654e0ac] _______________________________

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