On 03/03/2015 10:43 AM, Sarah Finnegan wrote:
> 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.
This does not surprise me too much. The mask will be very thin and
you'll have to make sure to sample it properly. So, try running
mri_vol2surf with V2_lh.mgz as the input and a projection fraction of
0.5. Then load the result as an overlay in tksurfer, eg,
tksurfer V2_subject5_1 lh inflated -overlay yournewfile.mgz -fminmax 0.5 1
>
> 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.
You'll need to decide what space you want to do the masking in. The way
you have it now, you have the mask in volume space and the thing to be
masked in surface space (thus the dimension error).
doug
>
> 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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422
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