Freesurfer

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30084 discussions

missing files in he v6 fsaverage on the Martinos Center network
by Douglas N. Greve 22 May '20

22 May '20

Sorry, I accidentally deleted some files from the v6 fsaverage located on the Martinos Center network. They have been restored, but it might have caused your recon-all process to fail if you had one running last night. Have a good weekend doug

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qcache error
by Wang, Lily 22 May '20

22 May '20

Hi FreeSurfer team, I am trying to run qcache but it is exiting with errors because it is not able to find files in the fsaverage/surf directory. I looked in $FREESURFER_HOME/subjects/fsaverage and there is indeed not a surf folder. Should I use one of the other directories like fsaverage3? Thanks, Lily

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Permutation Simulation Question
by Purcell, Juliann 22 May '20

22 May '20

External Email - Use Caution Hello FreeSurfer Experts, When we specify the number of spaces in running permutation simulation (i.e., 2spaces or 3spaces), does the program use a Bonferroni adjustment to correct? I’ve seen a couple references to Bonferroni correction in the wiki pages related to simulation, but I wasn’t sure how that fit in with the simulation. Thank you for clarifying! Best, Juliann Purcell, MSc Doctoral Candidate Medical/Clinical Psychology Doctoral Program University of Alabama at Birmingham Department of Psychology juliannp(a)uab.edu<mailto:juliannp@uab.edu>

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FW: Motion correction files contain 0 0 0 1
by Camerino, I.L. (Ileana) 22 May '20

22 May '20

External Email - Use Caution From: "Camerino, I.L. (Ileana)" <I.Camerino(a)psych.ru.nl> Date: Friday, 22 May 2020 at 14:27 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Motion correction files contain 0 0 0 1 Dear Freesurfer developpers, I performed tractography analyses by using tracula implemented in freesurfer version 6.0. I am performing the quality check as suggested in: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs. The problem is that all my motion files (for all subjects) contain the same values: 0 0 0 1. I checked the archive but I could not find an answer to a similar question in there. Please could you suggest me what went wrong? is it possible to recalculate only the motion estimation without having to run again recon all? Thank you in advance Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition

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OHBM Brainhack registration is open!
by Remi Gau 22 May '20

22 May '20

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circular/cyclic color map for polar data in freeview
by Devavrat Vartak PhD 22 May '20

22 May '20

External Email - Use Caution Hello freesurfer community, I am trying to setup a retinotopy pipeline. I have analysed pRF data generating polar angle and eccentricity maps which I project onto an inflated surface / flattened surface in freeview. Is there a way to display a circular/cyclic colour map (for the polar angle data) in the overlay screen?, the existing 'colour wheel' option seems to be linear? Thank you! Best, DV

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Re: [Freesurfer] Infant Freesurfer: infant_recon_all error
by fsbuild 21 May '20

21 May '20

External Email - Use Caution Hello Fleur, You should be able to do, $ file `which infant_recon_all` .... and the output should tell you if it it is a csh script, a Bourne shell script, a binary, etc. Unless you explicitly made csh or bash your default shell, then at the dollar sign prompt the default shell in Ubuntu is "dash" and not bash or Bourne shell.   If the file command reports it's a Bourne shell then it might be a bash script.  Or a bash script with a hash bang line of /bin/sh will run using dash shell on Ubuntu and can exit with that error on bash syntax/grammar.  You can eliminate that possibility by first running bash, and then the script, $ bash $ infant_recon_all --s SUBJ --age AGE (with I presume arguments substituted for SUBJ and AGE) - R. Fleur Warton May 20, 2020 at 04:05         External Email - Use Caution        Hi, I recently installed the Infant FreeSurfer package. When I try to run infant_recon_all (specific command: infant_recon_all --s SUBJ --age AGE)  I get the error  if: Expression Syntax I tried switching shells from bash to tcsh but got the same error. The FreeSurfer version is freesurfer-infant-20200205My platform is Ubuntu 18.04 Any suggestions how to fix this? Kind regards, Fleur   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Open Postdoctoral Scholar Position
by Neva M Corrigan 21 May '20

21 May '20

External Email - Use Caution Open Postdoctoral Scholar Position The University of Washington Institute for Learning & Brain Sciences (I-LABS; http://ilabs.washington.edu/) located in Seattle, WA is seeking a Postdoctoral Scholar to conduct analyses of human MRI brain imaging data. I-LABS is an interdisciplinary research unit dedicated to discovering the fundamental principles of human learning, with a special emphasis on early learning and brain development. The Postdoctoral Scholar will contribute to a team responsible for creating breakthrough findings in infant, child and adolescent brain development. Applicants should have a Ph.D. in Psychology, Linguistics, Cognitive Science, Biomedical Engineering, Neuroscience, or relate field. Extensive prior experience in analysis of MRI data in a scientific setting is essential. Programming and scripting skills are required, with Matlab or Python as well as Unix scripting experience at a minimum. Familiarity with common MRI image processing software packages (such as FSL, SPM, ANTS, FreeSurfer, or AFNI) is a must. Previous experience in working with pediatric MRI data is highly desired. Full position details and application submission are available at: https://apply.interfolio.com/75530. Review of applications will begin May 1st, 2020; applications will be accepted until the position is filled.

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mris_register intermediate results display
by Chris Adamson 21 May '20

21 May '20

External Email - Use Caution Freesurfer devs, Apologies if this has already been asked. I'm looking for a way that I can look at the progress of mris_register to investigate the accuracy of registration. Given that the registration is done on the 2D parameterisations of the curvature maps, how can I take a spherical surface and write out a tif file with the curvature maps of the surface that I'm registering and the target surface. I presume I need to use mrisp_write but it is unclear how I choose the curvature map to write in the image. Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 21 May '20

21 May '20

External Email - Use Caution I apologize for resending all of this info, but my email is acting up and every time I try to respond to the other email, my Outlook freezes. Here is info from our thread. I modified it to include the analysis in which I found significant clusters (i.e., looking at thickness with only age and sex as covariates and not ICV): After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters. The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values accounting for age and sex (this is a three group design). The X matrix was 240x12 (see attached file) * Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3 * Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3 * Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3 * Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3 * Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3 * Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3 Your code: There is not an easy way to do it, but you can do it in matlab cd glmdir X = load('Xg.dat'); y = load('perm.th30.abs.y.ocn.dat'); beta = inv(X'*X)*X'*y; yhat = X(:,[1 2 3]*beta([1 2 3]) When running your code, below are the errors I got in Matlab. Do you know how I can fix the code? >> X = load('Xg.dat'); >> y = load('perm.th30.abs.y.ocn.dat'); >> y = load('perm.th30.abs.y.ocn.dat'); >> beta = inv(X'*X)*X'*y; >> yhat = X(:,[1 2 3]*beta([1 2 3]) yhat = X(:,[1 2 3]*beta([1 2 3]) ↑ Error: Invalid expression. When calling a function or indexing a variable, use parentheses. Otherwise, check for mismatched delimiters. Did you mean: >> yhat = X(:,[1 2 3]*beta([1 2 3])) Error using * Incorrect dimensions for matrix multiplication. Check that the number of columns in the first matrix matches the number of rows in the second matrix. To perform elementwise multiplication, use '.*'. >> yhat = X(:,[1 2 3].*beta([1 2 3])) Index in position 2 is invalid. Array indices must be positive integers or logical values. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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