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The main point is that, it is not about human brain here, so I don't know
if providing Tal Xform or talairach.m3z will work
Cheers,
Arsene
2018-06-04 23:11 GMT+02:00 Bruce Fischl :
> -parc_dir should really be "seg volume". It is the name in th
On 06/01/2018 10:34 AM, Funk, Quentin wrote:
>
>
> Freesurfer Experts,
>
>
> thanks for the response! There was no command for projabs, but looking
> through the help I think projdist was about what I needed?
>
Sorry, yes, my bad.
>
>
> I was also curious though if there were a way to get it in
On 05/31/2018 05:22 PM, James Gullickson wrote:
>
> External Email - Use Caution
>
> OK. Two follow-up questions.
>
> 1. What structures should I add up to get supratentorial? Are they
> just in aseg or do I also need aparc?
All things in the aseg except cerebellum GM and WM and brain st
On 06/04/2018 04:01 AM, zuxfoucault Wong wrote:
>
>
> Hi Freesurfer experts,
>
> I am trying to resample the cerebellum atlas
> Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> to fmriprep output volume
> ${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz.
This has nothing to do with the contrast. Try the suggestion that was
printed out at the end (ie, remove the mean from the age and divide by
the stddev)
On 06/04/2018 09:28 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> Dear Freesurfer developpers,
>
> I posted a while back asking h
It is not clear what the actual error is. Is there anything that gets
printed out to the terminal that is not in the log? Also, can you verify
that the disk is not filling up?
On 06/04/2018 04:53 PM, Hanna Vasilevskaya wrote:
>
>
> Good afternoon all,
>
>
> I am new to Freesurfer (using version
set the TMPDIR env variable to point anywhere you want
On 06/04/2018 02:57 PM, Jiahe Zhang wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> While running selxavg3-sess on a large functional scan (7 Tesla, 768
> time points), I got these errors
>
> gzip: stdout:
-parc_dir should really be "seg volume". It is the name in the mri dir of
the volume that contains the manual labelings.
xform we use to put it in Tal coords. We also usually iterate where we
build an initial atlas, then align all the volumes to it and rebuild, but
if you have talairach.m3z yo
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Hi Bruce,
Thanks for your promt answer... but what about the others questions? I mean
:
-parc_dir esegatlast \ # Is that the directory of my
segmented subcortical structures?
-xform talairach_one.m3d \ # All the files are aligned, s
Hi Arselle
the node_spacing is the mm resolution of the atlas Markov priors and
class-conditional densities, the prior_spacing is the same for the
classwise spatial priors
the equivalent for the surface is mris_ca_train. It takes annot files as
input
cheers
Bruce
On Mon, 4 Jun 2018, arsen
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Dear Freesurfer experts,
While running selxavg3-sess on a large functional scan (7 Tesla, 768 time
points), I got these errors
gzip: stdout: No space left on device
ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected 3257077248
It sounds
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Dear All,
I have a set of 7 NIIFTI images (0.5 mm isotropic) :
- 2 average brain images (one T1W_MPRAGE and one T2W_SPACE template )
- 3 Tissue Probability Maps (Gray Matter, White Matter, CSF)
- 2 Atlases (One for Gray matter structures and another f
Dear Freesurfer developers
Hi
We collect a new ASL sequence at Bay 4 with Prisma. The scanner outputs a 3D
mosaic. The problem is that unpacksdcmdir doesn't seem to work correctly on it
so it results to an error!
Is there any command other than unpacksdcmdir for unpacking the ASL scans?
Than
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Hi Freesurfer Experts,
I have a question about calculating voxelwise % change.
We have collected T1-MRI across 3 time points in a couple of subjects and the
aim is to produce individual surfaces/maps showing the % of cortical thinning
with respect
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Dear Freesurfer developpers,
I posted a while back asking how to control for scanner site in a
multi-centre study. I think I now understand the formatting to do so for
a DOSS model, but was wondering how this would look for a DODS model.
There are 6
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Hi Freesurfer experts,
I am trying to resample the cerebellum atlas
Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz to
fmriprep output volume
${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz. I was
wondering if the
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I'm a Philips user as well. Creating a hierarchical directory tree is
sufficient enough, but for one thing. Nifti files do not carry the
information normally stored in DICOM header, and FS-Fast requires the f.nii
to have embeded info about the repetitio
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