Thanks Bruce,
Much appreciated.
Cheers
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDW
Hi,
Yes you can use fslmaths and Ants ImageMath to make an ROI from the given
mni coordinates. The command is like
fslmaths MNI_T1...gz -mul 0 -add 1 roi xmin xsize ymin ysize zmin zsize
tmin tsize ROI_name.
For a box of 10mm , you can use fslmaths kernel boxv...
or for a sphere you can use Image
Hi Antonin,
the -noasegfusion is not really supported and a left over from initial testing
when we first developed the stream. I will take a look at it and probably
remove the flag (or implement it in a way that it really initializes with the
aseg from the base, although I think this is not de
Dear FreeSurfer support,
I am a new user of the Freesurfer program and attempted to install everything
this morning on my Mac OSx 10.11.6 (El Capitan). To preface everything, I
updated my XQuartz program before installing, and I do not have Matlab on this
computer and understand that I can’t us
Hi all,
I am trying to extract the volume from a FreeSurfer segmented scan within a
pre-registered mask region, but only within the cortex, and wanted to check my
command.
The mask is a binary mask (value of 1 across the mask) and is in the same space
as the orig.mgz file. It covers part of
Hi Derek - There's an inconsistency among the output volumes that are supposed
to be in diffusion space; some have 2mm iso resolution and some have .9x.9x3mm.
From the logs it looks like you reran some of the pre-processing steps
separately. If you ran some before resampling and some after, this
Thanks Anastasia! You seemed to have caught the issue. the dtifit files
were mistakenly generated from the anisotropic preprocessed image. I will
ensure the same voxel dimensions among all inputs and re-run. Will let you
know if that doesn't fix it!
All the best,
Derek
On Tue, Jan 17, 2017 at 10:
Good Afternoon Support Team,
Per step one of your PETSURFER tutorial, the command: gtmseg --s ?,
where the is the name of the subject that we had ran recon-all,
outputs the error as described in out.txt attached in this email. If you have
the time, it would be much appreciated if you can help
Hi All,
I have a analysed data from AD patients and healthy controls and want to do a
group analyses of cortical volume.
I have run qcache on each subject.
In the lh.volume.fsaverage.mris_preproc.log file,
mri_surf2surf --srcsubject AD1 --srchemi lh --srcsurfreg sphere.reg
--trgsubject fsav
Dear Martin,
thank you for the feedback. I read the wiki but the instructions concerning
aseg edits were not much clear for me. And, I was misinformed by -noasegfusion
option.
The pity with aseg errors is that with the current design and when the error is
large to affect surfaces in base, it i
Dear Freesurfer Community,
I am wondering if you have these anatomic ROIs
(https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) already done
for the 3D volumetric standard MNI brain (either ch2 single subject
brain(preferred) or 152 average brain)
Greatly appreciated it.
Thanks and
Dear Freesurfer team,
I am wondering is there a way using tksurfer to edit a given atlas (for
example: destrieux atlas).
I would like to parcellate the superior temporal region into three regions .
Is there a way to do that?
Thank you
Aya
___
Fre
https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit
On 1/17/17 4:47 PM, Aya Kabbara wrote:
Dear Freesurfer team,
I am wondering is there a way using tksurfer to edit a given atlas
(for example: destrieux atlas).
I would like to parcellate the superior temporal region into three
Try running recon-all on the mni152 brain
On 01/17/2017 04:35 PM, Da, Xiao wrote:
>
> Dear Freesurfer Community,
>
> I am wondering if you have these anatomic ROIs
> (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation)
> already done for the 3D volumetric standard MNI brain (either
Dear Martin,
one more thing: When the error is large and present in both timepoints (as is
my case), I think that necessity of editing the same error in both timepoints
can easily lead to error (maybe even demonstrated as false positive effect)
caused by non-systematic editing. When editing com
Hi,
I've been trying to create WM lobes using the following steps:
1) mri_annotation2label --lobesStrict
2) Outputting the labels from step 1, & creating a simpler annotation without
limbic and insular lobes
3) Labeling the WM using mri_aparc2aseg (mri_aparc2aseg --s MySub --annot
Step2Anno
Hi Prad - mri_aparc2aseg assigns WM voxels to the nearest cortical region from
the cortical parcellation. Which cortical region would you want to assign the
corpus callosum to? What's labeled as corpus callosum in the aseg is the part
of the corpus callosum between the 2 hemis.
Best,
a.y
_
Hi,
>From whatever I read, there seem to be 2 ways for overlaying activation
maps on surfaces.
1) automatic/manual registration of activation volume to orig.mgz and usage
of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be
overlaid on an inflated surface in freeview or tksurf
Dear experts,
I have some questions.
I did Qdec group analysis with three nuisance factors. And one region
remained after FDR correction.
Then I did 'mri_surfcluster' specifying the FDR-determined voxel-wise
threshold as the --thmin.
After that I ran 'mri_segstats' and got the values.
1)Are these
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