Hi Doug, the Choi volume is in MNI152 space, not MNI305 space.

Hi Kathy, the correct command is "mri_vol2vol --mov $input --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o output1.nii.gz --no-save-reg --interp nearest"

Please note the use of the "--regheader" flag. The Choi volume is in exactly the SAME space as the $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz, it's just that the header information is different. Therefore the "regheader" flag takes care of that.

--Thomas

On Mon, Nov 11, 2013 at 7:40 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

Is the Choi2012 volume in fsaverage/mni305 space? If so, then the 2nd command is the right one. Use mri_binarize with the --match option to create separate masks. doug

On 11/11/13 2:24 PM, Kathy L. Pearson wrote:

...

To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I have tried both of the mri_vol2vol commands below. The results as shown in freeview are offset by several voxels from the original. Is there a transform or an intermediate step that can make this work -- or a different command? Also, is there a recommended way to extract each individual value (here 1 ... 7) to create separate masks in FSL 2mm space?

Thanks for any advice,

Kathy Pearson

#!/bin/bash input=$FREESURFER_HOME/average/Choi_JNeurophysiol12_MNI152/Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz mri_vol2vol --mov $input --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o output1.nii.gz --no-save-reg --interp nearest --precision uchar mri_vol2vol --targ $input --mov $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --inv --reg $FREESURFER_HOME/average/mni152.register.dat --o output2.nii.gz --no-save-reg --interp nearest --precision uchar

# Compare results freeview $input output1.nii.gz output2.nii.gz&

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This is expected, unfortunately. When you change the orientation, it changes the interpolation which changes things slightly. Those areas are all pretty small so the changes can appear to be large (though they are only a few percent).

doug

On 07/09/2014 01:42 PM, Kathy L. Pearson wrote:

I have run FreeSurfer 5.3 recon-all, getting different stats output, for these cases of anatomy input: (1) mprage DICOM series converted with dcm2nii (2) fslreorient2std (RL PA IS) on the dcm2nii output (3) mprage DICOM series converted with mri_convert

Differing example results include these from lh.BA.stats: case 1: BA1 1115 583 2017 2.511 0.650 0.175 0.155 66 9.1 BA2 3686 2392 5986 2.342 0.615 0.123 0.047 44 7.2

 case 2:
     BA1                                      1043    585   2060  2.569 0.637     0.181     0.226      169     4.8
     BA2                                      3569   2357   6064  2.397 0.612     0.123     0.050       38     5.9

 case 3:
     BA1                                      1071    558   1994  2.583 0.617     0.159     0.181       66     6.5
     BA2                                      3654   2364   6191  2.461 0.631     0.121     0.058       42     6.9

Is this as expected? Are there any options that I should apply to indicate that the orientation is RL PA IS if I use the same anatomy.nii.gz file in case #2 as prepared for FSL? Or must I always either use mri_convert to generate the input for recon-all? Or is there a command I should be running first to reset my RL PA IS image to a particular orientation required by recon-all?

Thanks,

Kathy Pearson

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