Thank you! Then I guess I would use the volume as the transform file to convert my mask.
Best, Idil ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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 >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
