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Hi Erez,
This should be answered in your other thread.

Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 15 Jun 2019, at 02:23, Erez Freud <[log in to unmask]> wrote:

Hi to all the FSL lords.

I am analyzing a dataset and I wish to register the tstat map produce from one run (at native space) to MNI space.

To do this, I used flirt as followed:


/usr/local/fsl/bin/flirt -in  tstatmap  -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out output  -applyxfm -init  featfolder/reg/example_func2standard.mat -interp trilinear'

The registration looks good, and then I moved to the second part of the analysis – extract the average t value for an ROI defined (by others) in MNI space.

To match the voxelsize and the field of view of the functional scan I applied the next transformation on the ROI file as followed.

/usr/local/fsl/bin/applywarp -i INPUTROI  -o  OUTPUTROIS -r feat folder/reg_standard/example_func.nii.gz  

Finally, I intended to run the featquery analysis but I get this odd error msg.

expected floating-point number but got "Mask"
   while executing
"format %.4g [ lindex $thevals 0 ] "
   ("for" body line 243)
   invoked from within
"for { set f 1 } { $f <= $featquery(multiple) } { incr f 1 } {

   #{{{ setup output dir and logging etc.

set mask $origmask

cd [ lindex $argv $f ]

I think that featquery wrongly identifies my mask as if it is in native space (I have validated, using FSLeyes that the mask is aligned nicely with the MNI152 template)

Will be happy to get your input

Thanks,
Erez Freud
York University,Toronto
[log in to unmask]

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