Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30078 discussions

Cannot create template when running longitudinal freesurfer 6.0.0
by Kilian Pohl 28 Jan '19

28 Jan '19

External Email - Use Caution Hi , The following command worked fine under 5.3.0 recon-all -openmp 88 -sd LAB_S00308/standard/20161209_2776_12092016/structural/longitudinal/freesurfer -base template_baseline_1 -tp baseline -tp 1 -all but now it produces there error ERROR: It appears that the -base templateID that you passed: -base template_baseline_1 is an existing regular (cross sectional) run! Please make sure you pass a new name (not one of the time points) for the template with -base. For example, if you are trying to create a -base: \' -base BertTemplate -tp Bert1 -tp Bert2 ... \' There is no existing regular (cross sectional) run. Do you know what the issue is ? The only dirs in LAB_S00308/standard/20161209_2776_12092016/structural/longitudinal/freesurfer are lrwxrwxrwx 1 djk root 100 Jan 28 10:29 1 -> ../../../../20161209_2776_12092016/structural/freesurfer6/LAB_S00308_standard_20161209_2776_12092016 lrwxrwxrwx 1 djk root 100 Jan 28 10:29 baseline -> ../../../../20080725_3594_07252008/structural/freesurfer6/LAB_S00308_standard_20080725_3594_07252008 drwxr-xr-x 3 djk root 23 Jan 28 10:29 template_baseline_1 Thanks Kilian

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Question regarding white substance with Freesurfer
by Erika Portera 28 Jan '19

28 Jan '19

External Email - Use Caution Good evening, I write you to resolve a problem with the program of freesurfer. Also following the tutorial for the corrections, I don't succeed in integrating parts of white substance. The problem concerns the underlying images ( error temporal gyrus sx) I thank you for your help. Erika Portera

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Italian Summer School: Interdisciplinary Research on Brain Network Dynamics
by Jovicich, Jorge 28 Jan '19

28 Jan '19

External Email - Use Caution Dear all, we are organizing an international summer school on interdisciplinary research oriented to the study of brain network dynamics (June 24-28, 2019). More information: https://event.unitn.it/brandyschool2019/ Feel free to disseminate to relevant groups. Regards, Jorge -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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Orientation by direction cosines
by Ritesh Mahajan 26 Jan '19

26 Jan '19

External Email - Use Caution Hello Team, Can any one please explain how we come to know whether it is RAI or RAS or any other orientation through direction cosines: Below is the direction cosine: I saw some non zero and negative values in non diagonal values of matrix. What does this signify ? 0.999377 0 -0.0352819 -0.00916448 0.965676 -0.259588 0.0340709 0.25975 0.965075 Suppose it is Head First Supine. Any help will be really appreciated. Thanks, Ritesh Mahajan

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dispaly retinotopy result
by starxifd 25 Jan '19

25 Jan '19

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FSFAST poor registration
by Keri Woods 25 Jan '19

25 Jan '19

External Email - Use Caution Hi I have a problem very similar to this one: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html I've tried the suggestions given there, but it didn't fix my problem. I'm running the FSFAST preproc-sess stream and the quality of the registration is very poor for most of the subjects. I've tried initializing the registration differently, using bbregister with --init-fsl, --init-spm and init-header, which didn't improve the results at all. I've also tried register-sess with --init-fsl, --init-spm and init-header, as well as spmregister-sess and fslregister-sess. Is there anything else I could try? Using the SPM GUI, the registration was fine, so I thought that spmregister-sess would have been an improvement, but it wasn't. Is there anyway I can import the registration obtained using the SPM GUI? Thanks for your help. Thanks, Keri

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Surface to volume conversion
by Bunting, Emma 25 Jan '19

25 Jan '19

External Email - Use Caution Hi! I’m trying to convert my sig.mgh output from GLM into a .nii file using mri_convert, and when I load the resulting volume in freeview this is what I see. The command I’m using is: mri_convert —in-type mgh —out_type nii.gz —out_orientation RAS /(root to sig.mgh file)/sig.mgh /(root to output file)/sig.nii.gz, Is there something I should be doing differently? Many thanks, Emma

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Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS
by falk.luesebrink＠med.ovgu.de 25 Jan '19

25 Jan '19

External Email - Use Caution Dear all, Has anyone run the longitudinal pipeline successfully using the WSL? I'm running it with Ubuntu 18.04.1 LTS and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I'm trying to process my first longitudinal data set following the instructions of the tutorial as close as possible. The data has been processed without issues and now I want to do the statistical analysis. When I run: long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR I get the following error: File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448 print '\nERROR: Specify --qedc (and other required arguments)\n' ^ SyntaxError: invalid syntax I get comparable errors for any other long_* command I try to run, e.g. long_qdec_table with or without any arguments gives: File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119 print '\nERROR: Specify --qedc' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('\nERROR: Specify --qedc')? Does anyone have a clue where this error originates from using either WSL or Ubuntu 18.04? Best, Falk ............................................... [klinikum_logo_schmal_e-mail_blau] Universitätsklinik für Neurologie Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg Telefon: +49-391-6117-512 falk.luesebrink(a)med.ovgu.de<mailto:falk.luesebrink@med.ovgu.de> http://www.kneu.ovgu.de/kneu.html

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Error in running make_average_subject
by Emanuel Alvaredo 25 Jan '19

25 Jan '19

External Email - Use Caution Hello!, I am getting the following error using the command make_average_subject mri/norm.mgz: could not load norm volume from (null) I have found this page with a path for de issue https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008… But I dont know how to apply the path. Can you give some information about this? Thanks! Emanuel

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move statistical map onto the cerebellum surface
by john Anderson 25 Jan '19

25 Jan '19

External Email - Use Caution Dear FS experts, I ran surface based PET analysis on subcortical regions. Then corrected the results for multiple comparisons using the method --grf in the command mri_glmfit-sim. I can visualize the output of multiple comparisons (i.e. the file grf.th1.3.pos.sig.cluster.mgh) on volume using tkmedit, this statistical map shows difference between the groups in the cerebellum.... Instead of visualizing the results on volume, I want to move this file to the cerebellum surface. I already created the cerebellum surfaces from aseg.mgz file in fsaverage using the command mris_tesselate. How can I move the the file grf.th1.3.pos.sig.cluster.mgh from volume space and map it on the cerebellum surface? I tried mri_vol2surf but this command requires the flag --hemi as a result it will map the file "grf.th1.3.pos.sig.cluster.mgh" on cerebral hemispheres (lh or rh) but not the cerebellum.. How can I map the file "grf.th1.3.pos.sig.cluster.mgh" on the cerebellum surface? Thanks for any suggestions, John

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Freesurfer