Freesurfer January 2023

freesurfer@nmr.mgh.harvard.edu

87 participants
111 discussions

VirtualBox ubuntu failed to start
by Casper Cappelen 28 Jan '23

28 Jan '23

External Email - Use Caution Hi, I am currently following the tutorial within your wiki at https://secure-web.cisco.com/1FhH_mVr-gZRnmOt8bSFGdT80u9kDmY3jmw7_fkHsGRV8q… I am reading the pdf-file Vbox_load_image.pdf at page 10, where I am attempting to boot up ubuntu. When pressing the Start button and choosing *ubuntu I get the screen shown below. How do I fix this, thanks. Best regards, Casper Cappelen [image: bilde.png]

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Request for password for extraction of .ova.7z file
by Casper Cappelen 27 Jan '23

27 Jan '23

External Email - Use Caution Hi, I am requesting the password to extract the image named "FS_7_2_0_ubuntu_18_04_06.ova.7z" Thank you, best regards, Casper Cappelen

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Re: [Freesurfer] Problem with quantifyHAsubregions.sh
by Georgina Angelopoulou 26 Jan '23

26 Jan '23

External Email - Use Caution Dear Eugenio, Thank you for your kindly reply. Actually, I tried both options and neither worked. When I renamed one subject and ran the following command, an error occurred. Please see below: Georginas-MacBook-Pro:ALBION georginaangelopoulou$ quantifyHAsubregions.sh hippoSf T1 -4393 testhippo.txt Gathering results from subjects in: testhippo.txt Using the prefix name: hippoSf Using the suffix name: T1 And writing them to: -4393 /Applications/freesurfer/7.3.2/bin/quantifyHAsubregions.sh: line 8: cd: testhippo.txt: No such file or directory failed to do cd testhippo.txt and then when I tried the following, another error occured: Georginas-MacBook-Pro:ALBION georginaangelopoulou$ quantifyHAsubregions.sh hippoSf T1 testhippo.txt -4393 Gathering results from subjects in: -4393 Using the prefix name: hippoSf Using the suffix name: T1 And writing them to: testhippo.txt /Applications/freesurfer/7.3.2/bin/quantifyHAsubregions.sh: line 8: cd: -4: invalid option cd: usage: cd [-L|-P] [dir] failed to do cd -4393 The second option with the script you sent me, did not provide any error, yet no output appeared. Could you please help me with that? Is there any possibility that this has to do with the version I used (7.3.2), using the following command: segment_subregions hippo-amygdala --cross 6608 Moreover, when compared this analysis with a previous version of Freesurfer, using the same subject, I noticed that all subfields’ indices are very similar except from three (Whole_hippocampus, Whole_hippocampal_body and Whole_hippocampal_head) for which all values were doubled compared to the previous version of FS. Could you please tell me why did this happened and which version should I trust? Apologies for such a long email. Thank you in advance. Best, Georgina

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Postdoc Position in Developmental/Educational Neuroscience at Vanderbilt
by Harriott, Emily M 26 Jan '23

26 Jan '23

External Email - Use Caution The Education and Brain Sciences Research Lab (ebrl.vkcsites.org<http://secure-web.cisco.com/1sAhpXZ8rNhkVyq6flvXlwsWY3bcq-8RYZjHqGrmm9cVYek…>) directed by Laurie E. Cutting, PhD, of Vanderbilt University in Nashville, Tennessee, USA, seeks a highly motivated postdoctoral researcher interested in developmental and educational neuroscience. The position provides an opportunity to work in a multidisciplinary research environment studying the neuroscience of child development, from birth through adolescents. Ongoing research includes 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; studies of typical and atypical reading and math development; and studies of other developmental disorders. Individuals will have the opportunity to work on large ongoing NIH-funded projects, including longitudinal neuroimaging studies focused on academic, cognitive, behavioral outcomes in early childhood development (starting at perinatal period) through adolescence. 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. Former post-doctoral fellows have been highly successful, including attaining tenure-track positions at R1 universities and getting independent NIH funding. 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. This fulltime position is appointed in one-year intervals, with re-appointments anticipated in years 2 and 3 (contingent upon satisfactory performance). Compensation is in line with NIH postdoc salary guidelines. Basic Requirements: • PhD in Neuroscience, Biomedical Engineering, Bioinformatics, Computer Science, Neuropsychology or related discipline. • Programming skills (e.g., Python, Matlab, R) • Demonstrated record of innovative scientific research in neuroimaging • Strong skills in the usage of one or more common neuroimaging packages (e.g., FSL, SPM, AFNI) • Strong communication skills in spoken and written English • Ability to work closely with an interdisciplinary team, providing training to students and researchers • Authorized to work in the United States If you are interested in the position, please email Laurie Cutting (Laurie.Cutting(a)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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Passcode of Ubuntu 7z file for VirtualBox
by Iara Senem 26 Jan '23

26 Jan '23

External Email - Use Caution Hi! I'm installing the VirtualBox version of Freesurfer (Ubuntu 18, the FS_7_2_0_Ubuntu_18_04_06.ova.7z file), and I would like to request the pass code to unzip the .ova file. Thank you, Regards, -- ____________________________________________________ Iara Senem Doutoranda da FMRP-USP Departamento de Neurociências e Ciências do Comportamento da FMRP Neuropsicóloga/Psicóloga - CRP 06/142554 Fone: +55 (16) 98209-1817

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MGH35 template in tracula
by Mark Wagshul 26 Jan '23

26 Jan '23

External Email - Use Caution Quick question - I'm looking for the T1 image that goes along with (i.e. in same space, or at least in same participants) as the MGH35_HCP_FA_template image which is used in TRACULA? Does anyone know where I can find this? Thanks! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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trac-all error
by Gonzalo Rojas Costa 26 Jan '23

26 Jan '23

External Email - Use Caution Hi: I tried to use trac-all using following syntax: trac-all -prep -s name -i SIEMENS_DICOM_256_GRADIENTS_TRACTOGRAPHY_FILES_PATH and I got the following error message: "ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction" Why? Sincerely, Gonzalo Rojas Costa

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Extracting Yeo network volumes for individual subjects
by Vyoma Shah 26 Jan '23

26 Jan '23

External Email - Use Caution Hi, How can I extract Yeo volumes by each network (for 7 or 17 network) for individual participants from FreeSurfer? I'm getting the same value for each participant, presumable because it's only pulling volumes from the template. Tried looking up the previous post with mri_surf2surf but am unable to successfully use this (or any other option) here. I have freesurfer_x86_64-7.2.0 and have run recon-all for each participant ('/user/fsrecons/outputs/<subj_ID>'). I have the Yeo annotation files (but do not have subject specific ones) such as in 'user/fsrecons/subjects/outputs/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot'. Each participant's aparc+aseg from the recon-all is in 'user/fsrecons/outputs/<subj_ID>/mri/aparc+aseg.mgz' Thank you so much!

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confirm 1651acc5c3dc6a2dda865be4528eeba83c3f81df
by Zhao, Don 25 Jan '23

25 Jan '23

External Email - Use Caution Hi, May I have the password for FS_7_2_0_ubuntu_18_04_06.ova? Thank you, Don

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ROI Analysis
by Beatriz Cavendish 25 Jan '23

25 Jan '23

External Email - Use Caution Hello FreeSurfer Community! I previously asked a question about volume quantification using an external atlas (in fact, there are 20 brain masks corresponding to the regions of interest). I managed to perform the quantification with the following commands and would like to know if everything is correct: Use mri_vol2vol to upsample to 1mm: /usr/local/freesurfer/subjects# mri_vol2vol --mov '/home/pedro/Downloads/Sallet_ROIs/Cluster1_L.nii' --targ '/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz' --regheader --o Cluster1_L_1mm.nii --interp nearest Use mri_vol2surf to create surface in XXX space: /usr/local/freesurfer/subjects# mri_vol2surf --mov Cluster1_L_1mm.nii --mni152reg --hemi lh --surf white --o lh.ROIA.mgh Visualize surface: /usr/local/freesurfer/subjects# freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.inflated:overlay='/usr/local/freesurfer/subjects/lh.ROIA.mgh' Convert surface to annotation file: /usr/local/freesurfer/subjects# mris_seg2annot --seg lh.ROIA.mgh --s fsaverage --h lh --ctab-auto --o lh.ROIA.annot Project the atlas to the subject's brain <https://secure-web.cisco.com/1JEN07txiABM5huyz9SEUPTihLYxW1TkkC2uDoF7TiUhSs…> : /usr/local/freesurfer/subjects# mri_surf2surf --srcsubject fsaverage --trgsubject bert --hemi lh --sval-annot fsaverage/label/lh.ROIA.annot --tval bert/label/lh.bert.ROIA.annot Calculate the atlas statistics <https://secure-web.cisco.com/1qVy6szcbmCutI-Y6GHK6daTo060hOEJXywT8OVArAV-2I…> : /usr/local/freesurfer/subjects# mris_anatomical_stats -th3 -mgz -cortex $SUBJECTS_DIR/bert/label/lh.cortex.label -f $SUBJECTS_DIR/bert/stats/lh.ROIA.stats -b -a $SUBJECTS_DIR/bert/label/lh.bert.ROIA.annot bert lh white Some questions: The projection of the mask volume in the MNI152 space onto the fsaverage space is fully matched. Are there any crucial differences between these spaces? How to get volume or surface file from annot file? Best regards, -- Beatriz Araújo Cavendish, MSc PhD student | Psychologist University of São Paulo São Paulo/SP - Brazil

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Freesurfer January 2023