Hello Doug,
Thank you for such a quick reply and for your insight.
I have adjusted the cmd but --fstarg seems to not be recognized as an
option ("ERROR: Option --fstarg unknown").
I also tried to include fsaverage following --fstarg, but I still received
the same error.
I am using stable53 and the usage of mri_vol2surf does not seem to include
--fstarg. Will using "--trgsubject fsaverage" instead of "--fstarg "
accomplish the goal of setting fsaverage as the target, or are there
additional details that I may be overlooking?
Please let me know what you think best!
Thank you,
Jacob
> The target has to be the freesurfer anatomical of the target subject
> (fsaverage in this case). You can get this by specifying --fstarg. The
> --reg is for the registration file; I'm surprised that the cmd actually
> ran. You just need to specify an output file with extension. Try the cmd
> below
>
> mri_vol2surf --mov /.../tstat2.nii.gz --fstarg
> --mni152reg --hemi rh
> --surf white --o /.../stats/output.mgh
>
>
> On 04/30/2014 11:55 AM, [email protected] wrote:
>> Hello Freesurfer Experts,
>>
>> I was wondering if someone can help me understand which options I need
>> to
>> include with mri_vol2surf for the following situation?
>>
>> I am trying to take group stats generated within FEAT that are in
>> MNI152_2mm space and registrar/project those to fsaverage inflated
>> surface.
>>
>> When I tried a quick visualization using just tksurfer and overlaying my
>> MNI space vol images, there seemed to be anatomical/registration
>> differences between where each space displayed the stats.
>>
>> I then attempted to use mri_vol2surf (command below) in hopes of better
>> aligning these two spaces, but the statistical intensity values have
>> been
>> lost and I am not confident that this command worked in the way I
>> thought
>> it might/would like it to.
>>
>> I am not sure which flags/options may be best in this situation, but any
>> insight you may have is greatly appreciated!
>>
>> Command used:
>> mri_vol2surf --mov /.../tstat2.nii.gz --ref
>> /.../MNI152_T1_2mm_brain.nii.gz --reg fsaverage --mni152reg --hemi rh
>> --surf white --o /.../stats/
>>
>> Is part of my problem that I have not specified a particular --out_type?
>>
>> Terminal Output:
>> srcvol =
>> /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/tstat2.nii.gz
>> srcreg = /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = rh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> Done loading volume
>> WARNING: the voxel resolution in the source volume (2,2,2) differs
>> from that listed in the registration file (1,1,1)
>> Reading surface
>> /space/sake/3/users/inverse/subjects/fsaverage/surf/rh.white
>> Done reading source surface
>> Mapping Source Volume onto Source Subject Surface
>> 1 0 0 0
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 21216
>> Writing to
>> /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/
>> Dim: 163842 1 1
>> non-standard value for imnr1 (1, usually 256) in volume structure
>> non-standard value for type (3, usually 0) in volume structure
>> non-standard value for width (163842, usually 256) in volume structure
>> non-standard value for height (1, usually 256) in volume structure
>>
>>
>> Outputed files:
>> COR-001
>> COR-.info
>>
>> Command used for viewing:
>>
>> tksurfer fsaverage rh white -overlay COR-001
>>
>>
>> Thank you for the help,
>>
>> Jacob
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> [email protected]
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [email protected]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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