Thank you for the help!
On Tue, Jun 14, 2011 at 9:10 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>wrote:
> **
> You should be able to use the reg and mni305.2mm.nii.gz in 4.5
> doug
>
>
> On 6/14/11 12:25 PM, Balaji Goparaju wrote:
>
> Thanks for the response! I seem to be getting better results.
>
> I was wondering if there was any way the same resampling can be achieved
> using Freesurfer 4.5 since a
> lot of analysis (including analysis with other tasks) has already been done
> in it, or if it is okay to use JUST the reg.2mm.mni152.dat file from
> Freesurfer 5.1 and keep the rest of the analysis the same as before?
>
> Thank you once again for this help!
>
> Regards,
>
> Balaji Goparaju
>
>
>
> On Tue, Jun 14, 2011 at 11:46 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> To go from mni152 to the MNI305 2mm space, use
>>
>> mri_vol2vol --mov mni305.2mm.nii.gz \
>> --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
>> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
>> --inv --o output.mni305.2mm.nii.gz
>>
>> This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the
>> mni305 2mm space.
>>
>> For your application, add --interp nearest, or use
>>
>> mri_label2vol --seg BA_mask.mni152.nii \
>> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
>> --invertmtx --o outfile.nii
>>
>> doug
>>
>>
>> Balaji Goparaju wrote:
>>
>>> Hello Freesurfers,
>>>
>>> I have Brodmann Area binary masks in the ICBM MNI 152 space, that I
>>> acquired using WFU_PickAtlas toolbox in SPM. These
>>> masks are .nii files, and have a RAS orientation.
>>>
>>> I am trying to resample these masks into the fsaverage MNI 305 space,
>>> specifically with the dimensions matching the "mni305.cor.subfov2.mgz"
>>> file found in the $FREESURFER_HOME/average file. This file is in the LIA
>>> orientation.
>>>
>>> However, the mni152.register.dat file seems to be transforming volumes
>>> from the MNI 305 space to the MNI 152 Space in LAS orientation
>>> (MNI152_T1_2mm.nii in FSL).
>>>
>>> Should I transform my Brodmann Area masks from the RAS orientation to a
>>> LAS orientation? If so, how can I achieve this? The RAS orientation is
>>> correct, so I know using mri_convert --out_dimension is out of the question.
>>>
>>> I have tried to use
>>> *mri_label2vol --seg {BA_mask} --temp
>>> {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg
>>> mni152.register.dat --invertmtx*
>>>
>>> Also, I have tried to use the inverted matrix from mni152.register.dat
>>> and use it with
>>> *mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o
>>> {output_file} --tal --talres 2*
>>> However, the output files had interchanged posterior (P) and anterior
>>> (A), and superior (S) and interior (I) orientations.
>>>
>>> What is the best way to achieve the resampling? Any guidance is really
>>> appreciated!
>>>
>>> Regards,
>>>
>>> Balaji Goparaju
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
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>>
>
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