Freesurfer March 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

recon-all errors after mri_pretess
by Alexopoulos, Dimitrios 07 Mar '22

07 Mar '22

External Email - Use Caution Hi, we're running FS 7.2 'recon-all -all' on a subject and are getting errors on our cluster (CentOS 8) The attached recon-all.log file is attached for details. The last several lines of the file are below. Any comments as to why its failing? Jim. pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 631 (out of 421942: 0.149547) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2022:03:03:12:51:58 mri_pretess N 4 e 3.84 S 0.01 U 3.70 P 96% M 56636 F 1 R 2214 W 0 c 330 w 325 I 8801 O 646 L 3.37 3.47 3.45 @#@FSLOADPOST 2022:03:03:12:52:02 mri_pretess N 4 3.37 3.47 3.45 #-------------------------------------------- #@# Fill Thu Mar 3 12:52:02 CST 2022 ________________________________ 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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fcseed with average data
by Marilena Wilding 07 Mar '22

07 Mar '22

External Email - Use Caution Dear FreeSurfers! I'm currently trying to do seed-based analysis. Therefore I'm using fcseed-config and fcseed-sess to configure my seed region. However, since I'm using a dataset that has been preprocessed with fMRIPrep, I'm having a lot of trouble doing this. Although I'm doing surface analyses, it seems that fcseed-sess is deriving the seed time course from the volumetric space (which of course makes sense since aparc+aseg is in volumetric space). I was wondering whether there is any way to use these functions with data, that has already been mapped onto the surface (i.e., fmcpr.sm0.fsaverage.lh)? The fMRIPrep output doesn't produce a template file, that seems to be indispensable for the formation of such a seed region. This is the code I used: fcseed-config -segid 1035 -fcname lh_insula_new.dat -fsd bold -mean -cfg mean.lh_insula_new.config -funcstem fmcpr.sm0.fsaverage.lh (I'm using funcstem since I don't have fmcpr.nii in my folders, only fmcpr.sm0.fsaverage.lh). fcseed-sess -sf sessid -cfg mean.lh_insula_new.config And this is my error: fcseed-sess -sf sessid -cfg mean.lh_insula_1010.config Logfile is /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/log/fcseed-sess.lh_insula_1010.dat.log Mon 07 Mar 2022 01:24:38 PM UTC Linux pslg067035.pers.ad.uni-graz.at 5.4.0-100-generic #113-Ubuntu SMP Thu Feb 3 18:43:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/structural/ cd /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project /usr/local/freesurfer/fsfast/bin/fcseed-sess -sf sessid -cfg mean.lh_insula_1010.config freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b Mon 07 Mar 2022 01:24:38 PM UTC Linux pslg067035.pers.ad.uni-graz.at 5.4.0-100-generic #113-Ubuntu SMP Thu Feb 3 18:43:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/structural/ cd /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project /usr/local/freesurfer/fsfast/bin/fcseed-sess -sf sessid -cfg mean.lh_insula_1010.config freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b mri_label2vol --seg /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/structural//01/mri/aparc+aseg.mgz --reg /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/register.dof6.lta --temp ERROR: could not determine file for /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/template --fillthresh .5 --o /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/tmp.fcseed-sess.470390/seg.nii.gz --pvf /storage/marilena/freesurfer_data/Study_3/Excite_data_3/Project/01/bold/001/tmp.fcseed-sess.470390/pvf.nii.gz ERROR: Option could unknown Thank you a lot in advance!! Best, Marilena

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recon-all permissions problems
by giuseppe messina 06 Mar '22

06 Mar '22

External Email - Use Caution hi i am a neurosurgeon, and i am a newbie in freesurfer, nut i thin i installed it appropriately and the licence txt file is ok i have a macbookpro 16 last generation with 32 gb of memory my freesurfer version is 7.2.0 the problem is that when i run recon-all ( in correct syntax) , permission issues appear; it seems that i dont have permissions to go ahead with the freesurfer. i also used ( as indicated in one of your tutorial ) the sudo chmod -R a+W $SUBJECTS_DIR command, but if i do so, a password is requested in the terminal. really, i dont know hot to solve this problem, please help me Giuseppe Thank you again -- Giuseppe Messina Dept Neurosurgery Istituto Nazionale Neurologico "Carlo Besta", Milan E-mail giusmex(a)gmail.com

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my email
by giuseppe messina 06 Mar '22

06 Mar '22

External Email - Use Caution hi my email is : giusmex(a)gmail.com thanx -- Giuseppe Messina Dept Neurosurgery Istituto Nazionale Neurologico "Carlo Besta", Milan E-mail giusmex(a)gmail.com

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Update on freeview error with M1 Macs running Monterey (MacOS 12.X)
by fsbuild 05 Mar '22

05 Mar '22

External Email - Use Caution Please check you have your freesurfer license file in a readable location, e.g., you can set the environment variable FS_LICENSE to point to the file license.txt in your home directory.  … in bash or zsh ...$ export FS_LICENSE=$HOME/license.txt… in csh or tcsh ...% setenv FS_LICENSE $HOME/license.txt The current development build of freesurfer now uses a newer version of the Qt distribution compared to the previous 7.2.0 and 7.1.1 releases.  You could try the development build to see if it remedies display issues with freeview on M1 Macs.. The package file  https://secure-web.cisco.com/1ZzEv2RHt0Q6Zowkpf2ipMDHM24zsuJwEJaPkN-sAc1WrZLf0pHDqrMdfHcwcLbdayl4GwciE3HSVe9hZ6mQiXeANHJpN--83bnCvOT7FTKOVmKgEurvQhXDpV-HLpvi7cy9mqEjbrM_QHH5YwMG_kxPyC9lM2wEFIgANTUhY1D78ULhUW3dmG3TLjm4OaYuVYHGjqEmJJD_VxOFIwA4suAJnq9KJ64uV-EQLOjZKIuS8imnZQmL6K9nd3ryadadTMaMdl7M87vojtuhub2Ub-P89vwRo_F2-DW6q4B4nhD_xSFSIMLZobD_0n84OPzF96jmVgKgNPDtsVf8YOoMydQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-darwin-macOS-dev.pkg%26nbsp; will install the development freesurfer distribution as /Applications/freesurfer/dev.  It will not interfere with or clobber your pre-exiting freesurfer 7.X X distributions installed as /Applications/freesurfer/{7.2.0, 7.1.1}. To switch to running the development build, (re)set FREESURFER_HOME in a new terminal window to /Applications/freesurfer/dev and then source the usual script to setup the freesurfer environment, e.g., source $FREESURFER_HOME/{SetUpFreeSurfer.sh, SetUpFreeSurfer.csh} I’ve tested running the freesurfer development build on a 2019 Intel MacBook Pro running Monterey.  That laptop uses an AMD Radeon 5500M graphics card with 4 GB of memory to drive both the laptop display (3072 x 1920 with 24 bit color) and a 2nd monitor (2560 X 1600 with a framebuffer depth of 30 bits).   Neither of those display are 4K resolution.  But I have not seen any issues with freeview displaying graphics on that 2nd monitor with the Intel MacBook Pro running MacOS Monterey, BigSur or Catalina. To completely remove the development build and the package file download you can do,$ sudo bash /Applications/freesurfer/dev/uninstall.sh$ rm -f $HOME/Downloads/freesurfer-darwin-macOS-dev.pkg - R. P.S. There have been reports of 2nd monitors with 4K resolution connected via USB-C cables causing Mac laptops running Monterey and BigSur to crash.  My understanding is that error is from the Mac graphics hardware not detecting the resolution of the 2nd display through that connection.   Switching to a USB-C to HDMI monitor connection fixed the issue for some users.  But I would avoid using a USB-C to USB-C connection for a 2nd monitor with 4K resolution.

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FreeSurfer VitrualBox VM Image password
by Gniewek Aleksandra (STUD) 04 Mar '22

04 Mar '22

External Email - Use Caution Dear all, My name is Aleksandra Gniewek and i am a student of the Warsaw University of Technology at the faculty of Electronics and Information Technology. I study Biomedical Engineering with a specialization in Biomedical Computer Science. I am currently writing an engineering thesis, the topic of which is based on the analysis of the functional examination of the visual cortex in fMRI. In my thesis I would like to use the set of tools included in Freesurfer. Therefore, I would like to request a password for Freesurfer VirtualBox Image to user 'developer', to be able to analyze fMRI photos. I download VM Image from page: < https://secure-web.cisco.com/1JazyfumX6KEWq94pvRyWOVtJLB1ldODBzyd2t-nUzm5RR… > and in accordance with the instructions (from the same page), I write an e-mail asking for a password to 'developer' user in UBUNTU. Thank you for your help. Aleksandra Gniewek [cid:image001.png@01D82FEA.DAC9F170]

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Postdoctoral Research Associate Dept. of Ophthalmology and Visual science University of Illinois at Chicago
by Nasiriavanaki, Zahra,M.D. 04 Mar '22

04 Mar '22

Postdoctoral Research Associate Dept. of Ophthalmology and Visual science University of Illinois at Chicago A post-doctoral position is available in the area of Stem Cell Therapy and Tissue Engineering at the Department of Ophthalmology. The research focuses on generating corneal organoids using novel 3D culture systems. Research experience in stem cell biology and regenerative medicine cell and/or molecular biology is necessary. Key Responsibilities/ Duties: • Collaborate with key personnel to meet research objectives • Collect, analyze, and interpret data • Perform laboratory experiments • Maintain lab notebook with recorded data • Publish original scientific research in peer-review journals • Present research findings at national/international scientific conferences • Other duties as assigned Minimum Qualifications: • Must have a PhD/Doctorate Degree in biology, biomedical engineering, or other related biomedical science fields. • Preference will be given to candidates with expertise in cell culture, immunohistochemical analysis, microscopy, western blot analysis, DNA and RNA purification, PCR, RT-PCR, ELISA, and/or basic bioinformatics. To apply, please send your cover letter describing research interests and accomplishments and CV to Dr. Elmira Jalilian, jalilian(a)uic.edu<mailto:jalilian@uic.edu> The position is supposed to be filled immediately.

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fspalm error
by Janina von der Gablentz 03 Mar '22

03 Mar '22

External Email - Use Caution Hi FreeSurfer community, I try to ues fspalm to correct multiple comparisons for a surface-based thickness analysis. Below is the code I use: python fspalm --glmdir Home/*/lh.group.glmdir --cft 1.3 --cwp .5 --onetail --name palm_onetail_1.3 --iters 1000 --2spaces The analysis starts successfully until runs "palm prep complete". Then it tries to run the generated matlab script. Matlab seems to start correctly. Afterwards I get the following error: Undefined function or variable 'palm', followed by this error: cannot find expected palm output "fsp_clustere_tstat_fewp_c1.mgz" . check for run_palm.m failures I guess there is a communication problem between the terminal and matlab/palm. Palm is included in the matlab path and I'am able to start palm within matlab. Any help with fixing this error would be appreciated. Thanks, Janina

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FW: Neurotechnology Job Opportunity for the BRAIN Initiative
by Fischl, Bruce 02 Mar '22

02 Mar '22

FYI From: Talley, Edmund (NIH/NINDS) [E] <talleye(a)ninds.nih.gov> Sent: Wednesday, March 2, 2022 1:08 PM To: Talley, Edmund (NIH/NINDS) [E] <talleye(a)ninds.nih.gov> Subject: Neurotechnology Job Opportunity for the BRAIN Initiative External Email - Use Caution I’m writing with information on a rare opening for a Neurotechnology Program Director to manage projects for the BRAIN Initiative. This is a dream job for anyone who wants to shape the development of cutting edge methods to understand the brain. The Brain Research through Advancing Innovative Neurotechnologies® Initiative (BRAIN Initiative), along with the NINDS Division of Neuroscience, is seeking exceptional candidates for the position of Neurotechnology Program Director (Health Scientist Administrator -13/14 or 15). This is a unique opportunity to advance the Neurotechnology portfolio for the BRAIN Initiative, a historic multi-billion-dollar effort to transform neuroscience by developing the technologies of the future. It offers collaborations with highly motivated, skilled, and scientifically curious colleagues from 10 NIH Institutes and Centers and from partner agencies such as NSF and DARPA. It requires extensive engagement and outreach to the research community to assess trends, communicate priorities, and identify new opportunities. Responsibilities include developing new programs, making funding recommendations, and direct managerial oversight of grants and research cooperative agreements. The position will be responsible for overseeing a portfolio of grants and cooperative agreements to support these scientific areas: neural interface technologies that record, modulate, or stimulate neural activity; novel materials and neural interface devices; and biotechnologies applied to the nervous system (including development of hardware, software, and computational techniques). Candidates should possess a doctoral degree and post-doctoral training, with expertise in research towards understanding and applying neural engineering concepts and technologies. We encourage applications from candidates who enjoy working collaboratively and bring a diverse perspective to neural engineering research. Job Post Link: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.ninds.nih.gov/About-NINDS/Jobs-At-NINDS/Health-Scientist-Admini…<https://secure-web.cisco.com/1FD1ESrT1kjS-AWTaloEZcV0Ogwza0WFHR-fbr8INZau1k…> Please send a letter of interest and curriculum vitae to Dr. Ned Talley at Edmund.Talley(a)nih.gov<mailto:Edmund.Talley@nih.gov>. Edmund (Ned) Talley, Ph.D. Program Director, National Inst. of Neurological Disorders and Stroke (NINDS) 6001 Executive Boulevard, Rockville MD 20852 Phone: 301-496-1917, Email: Edmund.Talley(a)nih.gov<mailto:Edmund.Talley@nih.gov> Alert: For BRAIN FOAs that require a Plan for Enhancing Diverse Perspectives (PEDP), applications without this new component will be withdrawn prior to review. Evaluation of the PEDP will be made during peer review as part of the scorable criteria and will be used to inform funding decisions. For more information: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://braininitiative.nih.gov/about/plan-enhancing-diverse-perspectives-p…<https://secure-web.cisco.com/18IFisnOCyk7RxokcMWlgoxS-RgdLRCD9bKVPSupLtv-6e…>

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Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!
by Knut J Bjuland 02 Mar '22

02 Mar '22

External Email - Use Caution Dear Freesurfer experts, I get this error when I am running FreeSurfer. Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /home/knutjb/subjects/test/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. It has a t1_sag_mprage sequence, and it also give this waning filesare not found to be different and cannot be sorted. In addition, I get these errors when importing using recon-all -i file -all -s test INFO: Found 770 files in //20210224_151919/5_t1_sag_mprage INFO: Scanning for Series Number 5 Scanning Directory INFO: found 768 files in series INFO: loading series header info. When I am running mri_concat --rms I am able to run recon-all -all. Your sincerely, Knut Jørgen Bjuland

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Freesurfer March 2022