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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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