The mask in volume format was created using a docker image and it works well both with my freesurfer origin and native volume files; the one that it doesn't align with is the volume file I am trying to adapt to/from a different software. The command line I used for transforming is this;
mri_vol2vol --mov native.template_areas.mgh --targ MW_IIHC_aTAL.nii --regheader --o template.mgz --no-save-reg
Best, Idil
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, August 17, 2017 6:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] mask alignment problem/mri_mask
Hi Idil
how did you create the mask and the transform? Also, you can't specify "%s" on the command line - you need an actual name of a transform file.
cheers Bruce
On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
A volume file I want to save as a mask(the orange/red shaded areas in the picture) on top of my volume file does not align as seen in the picture. I have used mri_vol2vol to align the mask to my native volume but apparently it did not work out. I am trying to correct this by using mri_mask now; I tried to use the option -xform %s which apparently applies the LTA transform to align mask to input volume, but now I get this error;
lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects/sub-01_MW/mri$
mri_mask -xform %s MW_IIHC_aTAL.nii native.areas_MW_aTAL.nii MW_aTAl_masked.nii transform file name is %s WARNING: hdr.dim[4] = 0 (nframes), setting to 1 niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm DoAbs = 0 Apply the given LTA xfrom to the mask volume Reading transform ... ltaReadFile(%s): can't open file No such file or directory mri_mask.bin: could not read transform file %s No such file or directory
I would deeply appreciate if someone could help me sort out this mess.
Thank you all! Best, Idil