sorry, I don't understand Bruce On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
Thank you!
Then I guess I would use the volume as the transform file to convert my mask.
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 6:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] mask alignment problem/mri_mask
ok, but your mri_mask command line has the string "%s" in it, which is not correct. You need to specify an actual file name. I also think you are better off using mri_convert -at <transform file name> .... to map the mask into the right coordinate system so that you can then view it in freeview to make sure it is correct
cheers Bruce On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
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
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