The command I used to visualise the label converted to volume form (using
mri_label2vol) in tkmedit was
tkmedit V2_subject5_1 orig.mgz -overlay V2_lh.mgz -overlay-reg register.dat
-fthresh .5 -fmid 1
my tksurfer command was
tksurfer V2_subject5_1 lh inflated
where I then attempted to overlay V2_lh.mgz as an overlay using the
register.dat file to register. This produces no visible overlay.
I have just retried with fill thresh set to 0 but no change to whether any data
is visible on the inflated surface.
V2_colour_lh.mgz is the functional overlay that I want to extract any data
active within V2 from, this was produced by my usage of mri_vol2surf
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {V2_colour_lh} --out_type {mgz}
essentially what I wanted was to take mask a functional volume of colour
activation across the occipital cortex with a V2 mask to only see activation
within V2 on the inflated surface.
I have a V2.label file and a V2_colour_lh.mgz file overlaid onto an inflated
surface using mri_vol2surf.
thanks
S
________________________________________
From: Sarah Finnegan
Sent: 03 March 2015 14:41
To: Freesurfer support list
Subject: RE: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Doug,
Thanks I had hoped to use mri_mask but was foiled in my attempt to convert the
.label files to .mgz using mri_label2bvol. I assumed I must be on the wrong
track.
my command was
mri_label2vol --label V2_lh.label --temp f.nii.gz --reg register.dat
--fillthresh .3 --proj frac 0 1 .1 --subject V2_subject5 --hemi lh --o V2_lh.mgz
I have previously used this command successfully to convert labels for usage in
FSL. The volume will display using tkmedit on the orig surface, but in tksurfer
using the inflated surface there is nothing visible when attempting to open as
an overlay.
I have played around with different options and attempted to move forward to
mri_mask using the V2_lh.mgz file (hoping to later open the data in tksurfer)
but the command
mri_mask -transfer 255 -keep_mask_deletion_edits masked_data V2_lh.mgz
lh_colour.mgz V2_colour_lh.mgz
gives
transfer mask voxels=255 to dst vol
Transferring mask edits ('1' voxels) to dst vol
ERROR: dimension mismatch between source and mask
I assume I must be missing something fundamental in the mri_label2vol command?
Thank you for your help
Sarah
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sarah Finnegan
[sarah.finne...@stcatz.ox.ac.uk]
Sent: 26 February 2015 15:12
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Bruce
Thanks for your reply,
I did use mri_vol2surf for the sampling
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {out file name} --out_type {mgz}
I don't believe that I want to average within the ROI. I want to take any
clusters of activity within V2 and feed this into a script i'm developing in
MATLAB to work out the distance between different voxel clusters and the size
of each cluster, but only for within my region defined as V2. Hopefully that
makes sense, If I average I think I will lose this spatial information?
Thanks
Sarah
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 26 February 2015 15:04
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Sarah
have you used mri_vol2surf to sample the data onto the surface? When you
say "extract specific regions of functional data from a flat " do you
want to average within the ROI?
cheers
Bruce
On Thu, 26 Feb 2015, Sarah Finnegan wrote:
> I have a question about the equivalent of fslmaths -mas option in
> freesurfer.
> I have several manually defined labels in .label form that I want to use to
> extract specific regions of functional data from a flat patch. Ordinarily in
> fsl I would just use
>
> fslmaths -invol {functional_data} -mas {bin_label} -outvol
> {masked_functional_data}
>
> but I'm a little confused about an equivalent for this in free surfer as I
> don't want to perform any further stats on these ROI yet, extract them from
> any surrounding data and overlay onto the flattened surface.
>
> I have tried using
> mri_vol2roi --label {V2_rh.label} --srcvol {functional_data.mgz} --srcreg
> {anat2exf.register.dat} --roiavg {func_V2_mask} --finalmskvol
> {func_V2_mask_out}
> but when overlaying the output file there are no data points visible.
>
> Any help would be great as several other functions that I have tried seem to
> be obsolete,
>
> Thanks!
> Sarah
>
>
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