Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

2 postdoc jobs at Cambridge University
by G. Murray 10 Feb '22

10 Feb '22

External Email - Use Caution 2 jobs, apply by 3rd March 2022 1) deep learning for automated variable sulcal segmentation. 18 month contract (in first instance). Working between Departments of Psychiatry (Suckling, Murray) and Computer Science ('Lio) in Cambridge. Collaboration with JF Mangin in Paris Neurospin. https://secure-web.cisco.com/1RzTC-fQjjzaLeLhUotLnD1_XftnjFj3jGKaC9bep28Wqw… 2) analysis of causes and cognitive and psychiatric consequences of sulcal variability. 36 month contract. Working with above post and further collaborators. https://secure-web.cisco.com/1LTVs5W0EsmnPabG_2tf8Pp46kt5MzX3fg3E2J4FeVJEd0… queries please to gm285(a)cam.ac.uk

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PETSurfer: error: MatrixReadTxT: could not scan value [1][1]
by Jennifer Bramen 10 Feb '22

10 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze amyloid PET data using PETSurfer. I am trying to do kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one using the wiki instructions and the other using the tutorial ROI-based approach) mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 --no-est-fwhm --nii.gz; done mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o $PET_DIR/PREV_019/mrtm1.roi --nii.gz;done Both times I get this error: error: MatrixReadTxT: could not scan value [1][1] I have opened all of the .dat files using my text editor (nano) and they seem ok. I have tried this in other subjects and I get the same error. I searched the list and I cannot find any discussion regarding this error using mri_glmfit and PET data. Anything you can do to help me troubleshoot this error would be greatly appreciated!!! Attached is my time.dat file (I think this is the most likely culprit). Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center

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infant freesurfer with --segfile flag
by Xiaoqian Yan 10 Feb '22

10 Feb '22

External Email - Use Caution Dear Freesurfer expert, I m running infant freesurfer with the --segfile option to do segmentations. The command I use is : infant_recon_all --s bbxx --age xx --segfile <our own segmentaion file> --forceskullstrip The results look great and the wm and pial surface align well with the segmentation file we used. However, I am wondering with this --segfile, which steps the infant_recon_all script is calling compared to those without calling the --segfile option. in addition, with the addition segmentation file provided, we found that the wm surface aligns too well with the 'aseg' file we provided with barely extra smoothing. We are wondering if we could submit our results for you to help us check if that looks reasonable to you. Thank you very much, Xiaoqian

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The fsaverage link points to an older freesurfer version
by Peled, Noam 10 Feb '22

10 Feb '22

Hello, I was running recon-all where SUBJECTS_DIR is /space/megraid/clinical/MEG-MRI/seder/freesurfer, where we store our patient's Freesurfer reconstructions. I received the following error: ERROR: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version Indeed, the fsaverage link points to version 6, where we are using 7.1.1 I think it makes sense to change it, but I don't have the permission to do that ( the owner is zkaufman, and the group is fsbuild) Thanks, Noam

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FREESURFER Using Freesurfer files within MATLAB
by Alison McDonnell 10 Feb '22

10 Feb '22

External Email - Use Caution Hi all, I am trying to use my Freesurfer files that were created during recon all in a MATLAB code. Do I need to add something at the start to do so or open MATLAB through the terminal to get these to work? At the moment it is giving an error saying "unrecognized function or variable" for fs_read_surf. Any help would be appreciated. Thanks, Ali

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Re: [Freesurfer] password for FS_Ubuntu_18_04_06.ova
by fsbuild 09 Feb '22

09 Feb '22

External Email - Use Caution Sending to your private email shortly.  Please note that the VM is currently setup to Freesurfer 7.2.0 out of the box. - R. On Feb 9, 2022, at 07:38, Deirel Paz Linares <deirel.paz(a)neuroinformatics-collaboratory.org> wrote:        External Email - Use Caution        Dear mailmanCould you please share with me the password for the user “developer” in the Ubuntu 18.04 Virtual Machine containing Freesurfer 6 “FS_Ubuntu_18_04_06.ova”? Best regards _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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password for FS_Ubuntu_18_04_06.ova
by Deirel Paz Linares 09 Feb '22

09 Feb '22

External Email - Use Caution Dear mailman Could you please share with me the password for the user "developer" in the Ubuntu 18.04 Virtual Machine containing Freesurfer 6 "FS_Ubuntu_18_04_06.ova"? Best regards

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macOS Monterey (Apple Silicon) and macOS Catalina (Intel-based), Freeview keeps crushing
by Kaya, Kutlu 09 Feb '22

09 Feb '22

Hi, I installed FreeSurfer version 7.2.0 via pkg file. FreeSurfer is working fine, but when I try to freeview either via terminal command or directly, it keeps crushing (please see the attached file). I uninstalled and re-install again. This time freeview is opening, but is still crashing. I’m using macOs Monterey with Apple Silicon. Although I’ve tried on macOs Catalina with intel-based, it still crushes. I’m not exactly sure what the problem is. Would you please help for it? Thank you so much! Kutlu

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PhD position in Developmental Cognitive Neuroscience
by Marisa Johanna Nordt 09 Feb '22

09 Feb '22

External Email - Use Caution PhD position in Developmental Cognitive Neuroscience Junior Group Leader Dr. Marisa Nordt in the Clinical Child Neuropsychology Section at RWTH Aachen University Hospital (Aachen, Germany) is currently recruiting a PhD student. Job description Our group is looking for a highly motivated and enthusiastic PhD candidate in the field of Developmental Cognitive Neuroscience. The successful applicant will work in a project investigating the effects of experience on human brain development with a focus on high-level visual perception (for example, perception of faces and written words) using a combination of different methods including (f)MRI and behavioral measures. The position is funded for 3 years and may be extended. Your profile * Master’s degree in Psychology, Biology, Computer Science, Cognitive Science, Neuroscience, or a related discipline * Attention to detail and the ability to work independently, as well as excellent communication and interpersonal skills * Interest in Developmental Cognitive Neuroscience and brain development * Strong statistical and methodological skills and interests * Knowledge of Matlab, Python, R, or a strong motivation to acquire these skills * Fluency in English and at least intermediate levels of German * Experience in working with children is a plus Your tasks * Learn how to design and conduct (functional) MRI studies in children and adults including behavioral assessments and apply advanced techniques to analyze these data * Presentation and publication of the results * Interaction with team members and international collaborators * We are a young, dynamic, and highly motivated team affiliated with the Clinical Child Neuropsychology Section at RWTH Aachen University Hospital, which provides an outstanding research environment with many opportunities for clinical research. Feel free to reach out to Dr. Marisa Nordt (mnordt(a)stanford.edu<mailto:mnordt@stanford.edu>) for more information. Applicants should email a CV, a letter of motivation, the expected date of availability and the names of two references as a single PDF to mnordt(a)stanford.edu<mailto:mnordt@stanford.edu> before March 5th 2022. The start date is negotiable, but earlier start dates are preferred.

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trac-all -prep with intrareg = 2
by Mirro, Amy 08 Feb '22

08 Feb '22

External Email - Use Caution Hello freesurfer devs, Thank you so much for all of your work on Tracula! I have been following this conversation (https://secure-web.cisco.com/1Ykw2-j5trx6ExR25illKidIACAuQbQ8aKBMO_GQNJvBet…) about an issue using flirt, and I am having a similar issue. It sounds like this user switched to bbregister, and that resolved the problem, but I was hoping to do a quick comparison between flirt and bbregister. I am running on Linux centos7 and my freesurfer build-stamp.txt is: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b. When I run trac-all -prep with flirt (setting intrareg = 2) , I get a set of errors of the following format: WARN: Could not open /export/freesurfer/freesurfer-7.2.0/trctrain/hcp/mgh_1010/syn/acomm.flt.prep.trk for reading WARN: Error was: Can not open file I think this is a result of the call the dmri_train (around line 2167 in trac-preproc on the 7.2 branch of your github). This call uses a trklist variable, which is set as follows: (around line 2109) set trklist = `printf $xspace/%s.$reg.prep.trk " $pathlist` Since I am running with flirt, the $reg here gets replaced with flt, so the code starts looking for .flt files inside the trctrain folder. As far as I can tell the trctrain directory only contains .bbr files. Should there be .flt files within this directory? Would it make sense to replace the $reg variable with a hard-coded '.bbr'? Or are the tracks that I should be using with flirt different from those that I should use with bbr? Thanks, Amy <https://secure-web.cisco.com/1Ykw2-j5trx6ExR25illKidIACAuQbQ8aKBMO_GQNJvBet…> ________________________________ 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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Freesurfer