[Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

2019-01-25 Thread falk.luesebr...@med.ovgu.de
[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.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> http://www.kneu.ovgu.de/kneu.h

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

2019-01-25 Thread falk.luesebr...@med.ovgu.de
in this email is strictly forbidden. - On 25 Jan 2019, at 10:26, falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> wrote: External Email - Use Caution Dear all, Has anyone run the longitudinal pipeline succes

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

2019-01-25 Thread falk.luesebr...@med.ovgu.de
falk.luesebr...@med.ovgu.de Gesendet: Freitag, 25. Januar 2019 10:42 An: Freesurfer Mailinglist Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS External Email - Use Caution Dear Juergen, Thanks for your quick reply! Actually

Re: [Freesurfer] Freesurfer Recon-all error

2019-02-01 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Kevin, just an educated guess, but did you copy the line "recon-all -all -i 758251.dcm -s Subj14" from somewhere (e.g. word)? Because it seems the dash in front of each flag is an emphasized dash, probably resulting in the error. Try the followin

Re: [Freesurfer] Problem with freeview in linux subsystem for windows

2019-02-20 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Brady, do you run a X server on windows? I run Xming and included in the .bashrc "export DISPLAY=localhost:0.0". Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Williamson, Brady Gesendet: Dienstag, 19. Februar 2019 21:51

Re: [Freesurfer] recon from 7T data

2019-03-26 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Valeria, you can account for the inhomogeneities Bruce was talking about by either using SPMs or FreeSurfers inhomogeneity correction. Personally, I prefer SPM over FreeSurfer, but if you supply a brainmask to the FreeSurfer tool, it gives reason

[Freesurfer] Primary slice direction and image origin?

2019-05-02 Thread falk.luesebr...@med.ovgu.de
... [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.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de>

Re: [Freesurfer] Primary slice direction and image origin?

2019-05-03 Thread falk.luesebr...@med.ovgu.de
image origin? On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote: > > External Email - Use Caution > > Dear all, > > This is not directly related to FreeSurfer, however, can anyone tell > me how the primary slice direction and image origin is determined from >

[Freesurfer] Longitudinal processing

2019-05-09 Thread falk.luesebr...@med.ovgu.de
. 44 39120 Magdeburg Phone +49-391-6117-512 falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> http://www.kneu.ovgu.de/kneu.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Primary slice direction and image origin?

2019-05-09 Thread falk.luesebr...@med.ovgu.de
something else (LPS maybe), so the "first voxel" might not be the same. On 5/3/2019 3:01 AM, falk.luesebr...@med.ovgu.de wrote: > External Email - Use Caution > > Hi Doug, > > thanks for your answer. I know how to print the slice direction, however, as > th

Re: [Freesurfer] Primary slice direction and image origin?

2019-05-09 Thread falk.luesebr...@med.ovgu.de
If S, then axial On 5/9/19 5:52 AM, falk.luesebr...@med.ovgu.de wrote: > External Email - Use Caution > > Thanks Doug, I think I may have resolved my orientation / transformation > issue. > > Do you happen to know how the primary slice direction is deter

Re: [Freesurfer] Longitudinal processing

2019-05-13 Thread falk.luesebr...@med.ovgu.de
effects (see https://www.ncbi.nlm.nih.gov/pubmed/26381562 ). Best, Martin On Thu, 2019-05-09 at 09:51 +, falk.luesebr...@med.ovgu.de wrote: > External Email - Use Caution > Dear all, > > I’m a beginner in using the longitudinal processing pipeline (as well >

Re: [Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy

2019-05-21 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Dear Gaurav Verma, this should fix your issue: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Verma, Gaurav Gesendet: Dienstag, 21. Mai 2019 17:34 An: freesurfer@n

Re: [Freesurfer] Change image orientation

2019-07-05 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Miguel, this should work with mri_convert --in_orientation RAI t1.nii t1_RAI.nii. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Miguel Ángel Rivas Fernández Gesendet: Freitag, 5. Juli 2019 11:00 An: Freesurfer support li

Re: [Freesurfer] recon_all hires

2019-08-21 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Mona, Potentially you have a bad skull strip resulting in a huge defect which will take a long time to correct. Simply fix your skull strip and you should be fine. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Nasiriavan

Re: [Freesurfer] How to fasten recon-all execution time without using CUDA

2019-09-18 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Vasudev, in case you use v6, you can use the -parallel flag to process the hemispheres (and a few other things if I remember correctly) in parallel. Note that doing so will parse the -openmp flag to all instances. E.g. recon-all -all -openmp 4 -p

Re: [Freesurfer] Freesurfer 7T MPRAGE

2020-01-06 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Dear Manoj, in case you want to rely on tools provided with FreeSurfer only, N3 can produce good results even for 7T data. However, in my experience, you need to supply a brainmask to N3 to achieve very similar results compared to SPM. Otherwise, e

Re: [Freesurfer] bias correction on 7T MEMPRAGE

2020-02-20 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Dear Vale, using the GUI of SPM you cannot get a FWHM of lower than 30. You have to save the batch to disk, load it in MATLAB and change the parameters to your liking. In case this sounds too complicated, you can use part of a reconstruction pipelin

Re: [Freesurfer] use of ANTs Denoising in FS 7.1

2020-08-25 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Dear Jim, I had been looking at the effect of denoising the data to improve processing speed in case of noisy data in an ISMRM abstract couple of years ago. However, I haven't had the time to follow up on this. Glad to see something similar now bein

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

2020-09-09 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Jim, The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm

Re: [Freesurfer] recon-all for 0.85 isotropic images error (bump)

2020-11-17 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Dear Kristine, I haven't had any issues processing high resolution data with version 6 or 7 using either the -cm or -hires flag. However, I never used the -cw 256 flag as my FoV was never greater than 256. Could you post the size of the created fi

Re: [Freesurfer] data sharing of freesurfer processed data

2021-02-03 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Stacey, aren't participant IDs already anonymized or at least pseudonymized? In any case, if that ID is part of the file name, you should delete or change the recon-all.cmd, recon-all.done, recon-all.log files as the input file name is written in

Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-19 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Nathan, are you sure that the SPM segmentation and the wm.mgz share the same space? You could try e.g. mri_convert -rl wm.mgz your_spm_segmentation.nii spm_wm.mgz Best, Falk Von: freesurfer-boun...@nmr.mgh.harv

Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-19 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Falk, Thank you for the response! I have given your suggestion a try and I am still getting the following error: free(): double free detected in tcache 2 Command terminated by signal 6 Best, Nathan From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf o

Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-23 Thread falk.luesebr...@med.ovgu.de
ppears to happen when I try to replicate those steps (with those included I hit no errors but the outputs are unchanged from before I incorporated the SPM file). Best, Nathan From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of falk.luesebr...@med.ovgu.de Date: Thursday, 20 January

Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-23 Thread falk.luesebr...@med.ovgu.de
falk.luesebr...@med.ovgu.de Gesendet: Montag, 24. Januar 2022 08:41:15 An: Freesurfer support list Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer External Email - Use Caution Hi Nathan, well, once again, I can't be much of help with regards to your error message. Hav

Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-27 Thread falk.luesebr...@med.ovgu.de
that the wm.seg.mgz might need to be uchar (a relic of when computers did not have so much memory). If it does not work with falk's command, you can try mri_convert -odt uchar --no_scale 1 wm.seg.mgz wm.seg.mgz On 1/24/2022 2:47 AM, falk.luesebr...@med.ovgu.de wrote: > External Ema

Re: [Freesurfer] mri_normalize error MP2RAGE

2022-01-31 Thread falk.luesebr...@med.ovgu.de
External Email - Use Caution Hi Cornelius, this doesn't address your issue directly and I may have simply been lucky, however, I haven't had any difficulties to process (7T) MP2RAGE data after background removal suggested by Marques et al. (https://secure-web.cisco.com/1fEVC_x

Re: [Freesurfer] parallel make_average_subject

2022-04-12 Thread falk.luesebr...@med.ovgu.de
C93ZvXasDk-IIz5wDknm4AQlXXC_a93P9uOhe8EQOOrfGk5_OG01Zna1rKjcSLKqr4YJ_UMCr1veLOpEuEx6gHH58wMQPWNtmH9m9_8Vn3t-sHBByWOIFliA/http%3A%2F%2Fwww.med.ovgu.de%2Funimagdeburg_mm%2Fummd_focus.gif] Universitätsklinik für Neurologie Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg Telefon: +49-391-6117-512 falk.luesebr...@m

Re: [Freesurfer] Reversing mri_convert

2022-05-05 Thread falk.luesebr...@med.ovgu.de
Telefon: +49-391-6117-512 falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> http://secure-web.cisco.com/1Ot95tcBSI8NwAu9j3-MCi-WNazHI1x3J_Wd7KLcLqqDxbYOgUclzwlyOXOLYHH412QcBGDnXDUOxzgguWCcQel8L9ZaACvmWHS4zTEdK8m4QYnGS7xdkGY5RGp0vFAppqrzydZAf5JmpYcPyBnyWZKvGyEXVs

Re: [Freesurfer] Recon-all Freezes on Parallel

2022-05-10 Thread falk.luesebr...@med.ovgu.de
Neurologie Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg Telefon: +49-391-6117-512 falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> http://secu