[Freesurfer] Using FS v5.3 for group analysis with recon-all done with FS v5.0

Dear experts, I'd like to use Freesurfer v5.3 to make group analysis on quantitative CBF maps computed in volume and projected on fsaverage surface. Knowing that all my subjects have been recon-all with FS v5.0, is this neccesary to me to relaunch recona-all to all my subjects with FS v5.3 before

Re: [Freesurfer] recon-all normalization: bias field output

Dear Freesurfers, The recon-all.log does not give info about the intermediate outputs (like nu2_est and nu2_field mnc-files), could you please confirm that the nu2_field.mnc is the bias field volume? It is the biggest file of all and is one of the last files generated by the script, but I would li

Re: [Freesurfer] Using FS v5.3 for group analysis with recon-all done with FS v5.0

No, you can use 5.3 group analysis with 5.0 data doug On 8/29/14 4:28 AM, Matthieu Vanhoutte wrote: Dear experts, I'd like to use Freesurfer v5.3 to make group analysis on quantitative CBF maps computed in volume and projected on fsaverage surface. Knowing that all my subjects have been re

Re: [Freesurfer] Using FS v5.3 for group analysis with recon-all done with FS v5.0

Thank you Doug ! Matthieu 2014-08-29 11:26 GMT+02:00 Douglas Greve : > > No, you can use 5.3 group analysis with 5.0 data > doug > > > > On 8/29/14 4:28 AM, Matthieu Vanhoutte wrote: > >Dear experts, > > I'd like to use Freesurfer v5.3 to make group analysis on quantitative > CBF maps compu

[Freesurfer] Post-doctoral opportunity (and beyond) in neuroimaging analysis

PostDoc (or beyond) in Neuro Image Analysis: Magnetic Resonance Imaging – Code 1267/2014/8 Description: Population Health Sciences at the DZNE aims to investigate causes and preclinical biomarkers of neurodegenerative diseases, and to study normal and pathological brain structure and function o

[Freesurfer] mri_preproc

Hello, I was still wondering about vertex selection after spherical registration. Once the brains are registered to the same spherical coordinate system, how are the vertices chosen? I noticed that each individual brain initially has a different number of vertices, but in the mri_preproc output fi

[Freesurfer] mri_watershed: really bad skull stripping

Hello, I’m new with FreeSurfer and I’m getting a really bad skull stripping (almost nothing) with mri_watershed –atlas in images converted from DICOM to .mgz with mri_convert. I lowered the threshold but did not improved considerably. I have tried with a subject from the tutorial dataset and

Re: [Freesurfer] mri_watershed: really bad skull stripping

Hi Arsula are you running this through recon-all or outside of it? The skull stripping works better after the intensity normalization that is part of recon-all cheers Bruce On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote: Hello, I’m new with FreeSurfer and I’m getting a really bad sku

Re: [Freesurfer] recon-all normalization: bias field output

Hi Barbara, Hang on, this will be slightly hairy. Right now, if you're not using the -3T flag when you run recon-all, you're essentially invoking N3 four times (the N3 wrapper, mri_nu_correct.mni). Every time you invoke N3, the output files are stored in separate directories (the once you located

Re: [Freesurfer] mri_watershed: really bad skull stripping

Hi Bruce, thank you very much for your fast answer. I'm running outside recon-all, only with mri_watershed. Thanks, that could help. Which are the options for recon-all if I have already the .mgz file?, I'm getting errors, appart from the warning for updating tcsh. Cheers, Ursula Date: Fri, 2

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? T

Re: [Freesurfer] mri_watershed: really bad skull stripping

you can give any format we support to recon-all as the input, including .mgz cheers Bruce On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote: Hi Bruce, thank you very much for your fast answer. I'm running outside recon-all, only with mri_watershed. Thanks, that could help. Which are the options

Re: [Freesurfer] mri_preproc

It is based on the 12th order icosahedral surface from which the surface atlas is constructed (fsaverage). doug On 8/29/14 4:06 PM, shinj...@andrew.cmu.edu wrote: > Hello, > > I was still wondering about vertex selection after spherical registration. > Once the brains are registered to the sam

[Freesurfer] Longitudinal troubleshooting

Hi Martin and all, I am about to process a large longitudinal dataset (normal development, no patients) and wanted to ask about the best (i.e., time efficient) strategy for troubleshooting. If I understand correctly from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits, it might be

[Freesurfer] Reconstruct tm3d warp from mri_cvs_register

Hi all, I ran mri_cvs_register but forgot to add --nocleanup. I have the final combined m3z and no tm3d, and for el_reg just mgz files. Can I recreate the tm3d combined with just these files? On the wiki it says use createMorph - I tried different inputs in 5.3 and dev environments with no succes

Re: [Freesurfer] Longitudinal troubleshooting

Hi Janosch, yes, that works if longitudinal changes are really small. You should be careful with copying edits from base to the long as even with small atrophy there can be local deformations of the brain, and rigid alignment and copying may not make sense. Yet, I believe that even without cop