Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30065 discussions

bash: recon-all -İ : command not found
by behçet ayyıldız 13 Feb '23

13 Feb '23

External Email - Use Caution Hi dear all, I got the similar problem. I have freesurfer version 7.1.1 and when I was trying to run the "recon-all" it indicates me that the command not found. Here below you can find all that bash indicates. -------- freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /sw/freesurfer/7.1.1/ FSFAST_HOME /sw/freesurfer/7.1.1/ FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /sw/freesurfer/6.0.0//subjects MNI_DIR /sw/freesurfer/7.1.1//mni FSL_DIR /sw/fsl/6.0.5.1 drodriguez@causal:~$ cd ../../.. drodriguez@causal:/$ cd data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD/ drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ export SUBJECTS_DIR=`pwd` drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ echo $SUBJECTS_DIR /data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ recon-all-i pat_CoDa85.nii -s pat_CoDa85 -all bash: recon-all-i: command not found thanks.. -- *Behçet Ayyıldız..*

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ScLimbic: error: could not allocate memory for slice 1 out of 256error: mri_convert --conform failed!
by stdp82＠virgilio.it 13 Feb '23

13 Feb '23

External Email - Use Caution Hi list, the error is reported below. Of note I have just runned, with success, ScLimbic for another study. Thus, I do not understand which is the issue for this one. Thanks Stefano mri_sclimbic_seg --i FOLDER --o FOLDER --write_volumes --write_qa_stats --etiv --conform /Applications/freesurfer/7.3.2/sclimbic/python/scripts/mri_sclimbic_seg --i FOLDER --o FOLDER --write_volumes --write_qa_stats --etiv --conform Excluding seg [853]Using CPUUsing 1 thread(s)Loaded lookup table /Applications/freesurfer/7.3.2/sclimbic/models/sclimbic.ctab Loaded population stats /Applications/freesurfer/7.3.2/sclimbic/models/sclimbic.volstats.csv Loaded model weights /Applications/freesurfer/7.3.2/sclimbic/models/sclimbic.fsm+ad.t1.nstd00-50.nstd32-50.h5 Computing etiv from scratchmri_convert --conform FOLDER/subjID.mgz /var/folders/vd/g4zth0dn6nldcx62m0l827sr0000gn/T/tmpk6kr248m/nu.mgz reading from FOLDER/subjID.mgz...error: could not allocate memory for slice 1 out of 256error: mri_convert --conform failed!

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ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage
by Lizanne Arnoldy 13 Feb '23

13 Feb '23

External Email - Use Caution Dear freesurfer Experts, I’ve been trying to run the fMRIPrep container on multiple subjects using two different versions of fmriprep (fmriprep-22.0.2.sif and fmriprep-22.1.0.sif) on a Linux computer. Most of the time, the container runs without errors, however occasionally, it exits with the error message: “ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version” I have checked the mailing list where this error has been mentioned but haven’t found the solution yet. Here’s some additional information that might be helpful: - The …/fmriprep/sourcedata/freesurfer/sub-096/label directory, the rh.BA1_exvivo.label file is present (and has viewing permissions), but the lh.BA1.label file is missing (not sure if this needs to be included). * The recon-all log file has been attached I would appreciate any insight or guidance on what may be causing this error and hot to resolve it. Best, Lizanne

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(no subject)
by behçet ayyıldız 13 Feb '23

13 Feb '23

External Email - Use Caution behcetayyildizz(a)gmail.com -- *Behçet Ayyıldız..*

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Freesurfer VM Archive Password
by Ali Muqtadir 13 Feb '23

13 Feb '23

External Email - Use Caution Hi, I was wondering if I could please get the password for the Freesurfer VM archive 'FS_7_2_0_Ubuntu_18_04_06.ova.7z' (if this is the right place to ask). Thank you! Best, Ali ________________________________ Scotland's University for Sporting Excellence The University of Stirling is a charity registered in Scotland, number SC 011159

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Recon-all exited with errors
by Goeckner, Bryna 10 Feb '23

10 Feb '23

External Email - Use Caution Hi All, I am using FS 7.2.0 and have one subject that exited recon-all with errors (looks like for talairach issues) but I am not able to use tkregister2 to view and make manual adjustments to the talairach since surf/lh.orig was not generated. I then tried recon-all with the -notal-check flag, which exited “without errors” although the talairach is nowhere near correctly aligned and while aparc & aseg in freeview appear ok, the brainmask appears to have issues (when I turn it off, the entire background displays as white). I’m including the recon-all logs (original & notal-check flag) and have listed the actual commands used below as well. Any help you can provide in figuring out how to run this subject is greatly appreciated. Thanks! The original code was: recon-all -subject subj# \ -i rawT1.nii.gz \ -T2 rawT2.nii.gz \ -T2pial \ -parallel -openmp 12 \ -3T \ -all And for the second run, -notal-check was added after -all For tkregister2: tkregister2 --s subj# --fstal --surf orig Bryna Goeckner (she/her) Graduate Student Meier Lab<https://secure-web.cisco.com/1pur5M1FnQYnB8iXyrOEPR6TC3h-zcLEgSRygNp0xNHDNF…> Medical College of Wisconsin Neuroscience Doctoral Program

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Postdoctoral Position Available in NYC, USA
by Tram Nguyen 10 Feb '23

10 Feb '23

External Email - Use Caution [image: image.png] The Biomarker and Dimensional Psychiatry Center at PRIME, a program within the Department of Psychiatry and Behavioral Sciences at Albert Einstein College of Medicine (Einstein), is seeking highly motivated postdoctoral scholars in the field of human *neuroimaging*. Available positions will focus on analyzing *fMRI* and proton *MR spectroscopy* data as well as acquiring or processing related MRI and biological measures. Candidates should either have completed or be near completing a PhD in neuroscience, psychology, cognitive neuroscience, radiology, engineering, biostatistics, or a related field, and should have a strong background in *quantitative analysis*. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome Workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/or R programming languages is a plus. The primary responsibility for this postdoctoral fellow will be to run scans, analyze neuroimaging data from multiple ongoing and recently concluded research projects, and write manuscripts. *The position is hybrid, and 2 days a week can be remote. Neuroimaging scans are conducted at the Leon and Norma Hess Center of the Icahn School of Medicine at Mount Sinai located in the Upper East Side, Manhattan. Salaries are highly competitive for the area!* Under the mentorship of Vilma Gabbay, MD and Benjamin Ely, PhD, postdoctoral scholars will be expected to advance *clinical* and *methodological* knowledge through their postdoctoral training. Our lab is dedicated to the study and treatment of *mood*, *anxiety*, and *substance use disorders* in *adolescent* and *high-risk adult* (e.g. HIV+) populations using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is dedicated to advancing the fields of magnetic resonance imaging and spectroscopy. The lab is funded by 5 ongoing NIH R01 studies (R01MH120601, R01DA054885, R01MH128878, R01MH131207, and R01MH126821) as well as an NIH center grant (P30AI124414) and several smaller grants, providing unparalleled funding for active and exploratory studies. Major research topics include longitudinal studies of adolescent mood and anxiety disorders; comorbidity of depression, cannabis use, and HIV infection; and an intervention study aimed at improving well-being among healthcare workers with parental responsibilities during the COVID-19 pandemic. Project abstracts with further details can be found on NIH RePORTER. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra/Prisma, Philips Elition) with cutting-edge accelerated and multi-echo fMRI sequences, high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The PIs are fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PI’s proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. The initial employment period for this position is two years, with the possibility of extension. Salary will be competitive and commensurate with experience and the cost of living in New York City. Subsidized housing dedicated to postdocs at the Rhinelander residence is available within walking distance to the Einstein campus in the Morris Park neighborhood of The Bronx. The position is hybrid, and scans take place at Mount Sinai in Upper East Side, Manhattan. Public transit options between Manhattan and the Einstein campus include the BxM10 express bus (stop right on campus) and the 2/5/6 trains. Please send a CV, statement of interest, and contact information for three references to gabbay.lab(a)einsteinmed.edu or vilma.gabbay(a)einsteinmed.edu. Albert Einstein College of Medicine is an equal opportunity employer, and all qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Compensation will be proportional to experience and exceed standard postdoctoral fellowship rates posted by Albert Einstein College of Medicine ($70,000 - $80,000).

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mri_easyreg tool
by Peters, Johnny Y 10 Feb '23

10 Feb '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use the mri_easyreg on the developmental version of freesurfer but I am confused about what .mgz or .nii(.gz) I am supposed to use for the reference image, floating image, and the others. I saw no previous threads on the mailing list addressing my question so I decided to email you. Would you be able to give an example command line using the subject bert in the freesurfer directory? Thank You

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Re: [Freesurfer] [FreeSurfer] Help on installation of Freesurfer on Ubuntu 18 on Windows 11
by fsbuild 10 Feb '23

10 Feb '23

External Email - Use Caution Hello Krystal, Doing an "upgrade" is fine, but I don't think you want to do a "dist-upgrade".   Telling the system to upgrade to the distribution likely installed something causing the conflict(s) when you tried to install the 7.3.2 release.  If you made a snapshot of the VM when you first booted it with 7.2.0 installed, then you could revert back to that snapshot.  You could revert back to any snapshot you made prior to the "dist-upgrade".   Otherwise, I think you will have to go back and make a new copy of the VM so that you are starting out with the system from the original disk image file. The I would try,$ sudo apt-get upgrade$ sudo apt-get install ./freesurfer_ubuntu18-7.3.2_amd64.deb - R. On 2/8/23 10:42, Krystal Xiwing Yau (krystaly(a)hku.hk) wrote:         External Email - Use Caution         Dear FreeSurfer users, I tried to install the newest version of FreeSurfer 7.3.2 on ubuntu 18..04.6 VB Image. I have run the following commands before installing: $ sudo apt-get dist-upgrade  $ sudo apt-get upgrade $ sudo apt-get install ./freesurfer_ubuntu18-7.3.2_amd64.deb

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Re: [Freesurfer] Freeview 'quit unexpectedly' before opening
by fsbuild 10 Feb '23

10 Feb '23

External Email - Use Caution When you say you are running Mojave, I think you probably meant to write 10..14.6 (not 10.16.6). You could check you have the latest version of XQuartz (2.8.5) installed from,https://secure-web.cisco.com/11eALbuyxL0_txSil8AchFZPgix3GCpAuJbqcYDFJ… You may need to reboot the machine after installing Xquartz. Once back up, open a new terminal window and run the bash shell, $ bash Try putting your license file, e.g., license.txt. in your $HOME directory, and then set the environment variable FS_LICENSE to its absolute path, e.g. $ cd $HOME$ head -1 license.txtme(a)somewhere.org.  <—— email address you used to register with $ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEme(a)somewhere.org.  <—— email address you used to register with Then the usual setup,$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Then try opening an empty Freeview window again,$ freeview - R. On Feb 8, 2023, at 14:28, Rankin McGugin <rankin.mcgugin(a)gmail.com> wrote:<freeview_2023-02-08-122744_Rankins-MacBook-Pro.crash>

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