Hi Cristian,

Can you upload your files for us?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Lilla

On Tue, 28 Feb 2017, Donos, Cristian wrote:

Hi, I was able to apply the morph using combined_toColin27_elreg_aseg.tm3d instead of fullCSVmorph.tm3d. The resulting coordinates are wrong, but it proves that memory is not an issue -  combined_toColin27_elreg_aseg.tm3d is 458MB, while fullCVSmorph.tm3d is only 50Mb.

So what else can be the issue?

Best, Cristian

applyMorph --template /Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz --transform combined_toColin27_elreg_aseg.tm3d point_list coords.txt transformed_coords.txt linear Template name:/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz After loading template Template name:/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz After loading template  extension = tm3d  data size = 110494908  uilen = 6  loading transform id string =   data size = 16  uilen = 3  loading transform id string =   data size = 20740581  uilen = 6  loading transform id string =   data size = 20473944  uilen = 6  loading transform id string =   data size = 20218265  uilen = 6  loading transform id string =   data size = 19973768  uilen = 6  loading transform id string =   data size = 19749328  uilen = 6  loading transform id string =   data size = 19541370  uilen = 6  loading transform id string =   data size = 19323542  uilen = 6  loading transform id string =   data size = 19131546  uilen = 6  loading transform id string =   data size = 18921656  uilen = 6  loading transform id string =   data size = 18764984  uilen = 6  loading transform id string =   data size = 18618427  uilen = 6  loading transform id string =   data size = 18553570  uilen = 6  loading transform id string =   data size = 18408866  uilen = 6  loading transform id string =   data size = 18337646  uilen = 6  loading transform id string =   data size = 18424799  uilen = 6  loading transform id string =   data size = 18774041  uilen = 6  loading transform id string =   data size = 20572783  uilen = 6  loading transform id string =   data size = 19438063  uilen = 6  loading transform id string =   data size = 71  uilen = 7  loading transform id string =   loaded transform  executing filter on file coords.txt  morph applied in 1.86923 minutes

  On Feb 21, 2017, at 11:10 AM, Donos, Cristian <Cristian.Donos@uth.tmc.edu> wrote:

Hi Lilla,

It’ s a Mac Pro with 64Gb Ram. Best, Cristian

Hi Cristian,

Can you send me the original mri_cvs_register command? When I apply the m3z transform to your moving volume the result is not registered to the target.

set morph = combined_toColin27_elreg_aseg.m3z set targ = N27orig.mgz set mov = TS076CDorig.mgz set out = ${mov:r}.2.${targ} mri_vol2vol --mov $mov --targ $targ --o $out --m3z $morph --noDefM3zPath

Lilla

On Thu, 2 Mar 2017, Donos, Cristian wrote:

I have uploaded the files i am using.

After updating to Freesurfer 6.0, i was able to use fullCSVmorph.tm3d, but the coordinates in the output file remain unchanged. The other tm3d files in my csv folder return 10000 10000 10000 for each point in the input txt file.

Best, Cristian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer