Freesurfer

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Freesurfer 7.1 hires error
by Jones, Richard 22 May '20

22 May '20

External Email - Use Caution I ran freesurfer 7.1 with the following options:- -i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR ./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T -mprage -FLAIRpial -hires -parallel -all The job failed, the logfile recon-all_hires.log is attached. I then reran the job with the same datasets but exchanged -hires with -conf2hires and used the subject ID TEST_050620c and the job completed successfully (the logfile for this job, recon-all_conf2hires.log, is also attached). Any idea what the problem is when using the -hires option? Thanks Richard

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 22 May '20

22 May '20

External Email - Use Caution I just tried the revised code, and it gave me the adjusted values for each cluster by group. Is there a way to get covariate adjusted values for each participant? --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Friday, May 22, 2020 10:09 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 195, Issue 54 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Freesurfer 7.1 hires error (Douglas N. Greve) 2. Re: question on partial volume correction (Barletta, Valeria) 3. Re: question on partial volume correction (Douglas N. Greve) 4. Re: Group Analysis Covariates (Hua, Jessica) 5. Re: Group Analysis Covariates (Douglas N. Greve) 6. Re: mris_register intermediate results display (Chris Adamson) 7. Open Postdoctoral Scholar Position (Neva M Corrigan) 8. Re: Infant Freesurfer: infant_recon_all error (Hoopes, Andrew) 9. Re: circular/cyclic color map for polar data in freeview {Disarmed} (Caspar M. Schwiedrzik) 10. OHBM Brainhack registration is open! (Remi Gau) 11. FW: Motion correction files contain 0 0 0 1 (Camerino, I.L. (Ileana)) ---------------------------------------------------------------------- Message: 1 Date: Thu, 21 May 2020 12:11:55 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer 7.1 hires error To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9eaf8c24-3b80-eb34-7cd0-09080c152b03(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" I don't know what is wrong. Can you upload the hires run? Instructions below From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log? into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 5/21/2020 9:35 AM, Jones, Richard wrote: > > ????????External Email - Use Caution > > I ran freesurfer 7.1 with the following options:- > > -i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR > ./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T ?mprage > ?FLAIRpial ??hires ?parallel ?all > > The job failed, the logfile recon-all_hires.log is attached. I then > reran the job with the same datasets but exchanged ?hires with > ?conf2hires and used the subject ID TEST_050620c and the job completed > successfully (the logfile for this job, recon-all_conf2hires.log, is > also attached). Any idea what the problem is when using the ?hires option? > > Thanks > > *Richard* > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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