External Email - Use Caution
Bruce,
this is the output:
mri_info wm.mgz
Volume information for wm.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 8.21 msec, TE: 3.22 msec, TI: 450.00 msec, flip angle:
12.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
-6.3280
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a =
28.2400
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
19.2471
talairach xfm :
/Users/davidemomi/Downloads/Broad_60_AV/60_AV/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 121.6720
0.0000 0.0000 1.0000 -99.7600
0.0000 -1.0000 0.0000 147.2471
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 -0.0000 -0.0000 121.6720
-0.0000 -0.0000 -1.0000 147.2471
-0.0000 1.0000 -0.0000 99.7600
-0.0000 -0.0000 -0.0000 1.0000
thanks
Il giorno ven 24 ago 2018 alle ore 18:02 Bruce Fischl <
fis...@nmr.mgh.harvard.edu> ha scritto:
> can you run mri_info on it? And please include the full screen output
> including the command line that you run as well as what it produces.
>
> thanks
> Bruce
> On Fri,
> 24 Aug 2018, Davide Momi wrote:
>
> >
> > External Email - Use Caution
> >
> > Yes, I meant the second one and rh.aparc.annot (not lh) given that as
> you said I specified rh.
> >
> > As for the ls -l on wm.mgz this is the output:
> >
> > -rw-------@ 1 davidemomi staff 432151 Jun 13 2017 wm.mgz
> >
> > Thanks
> >
> >
> >
> > Il giorno ven 24 ago 2018 alle ore 17:35 Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> ha scritto:
> > Hi Davide
> >
> > do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It
> should be the
> > latter, not the former. Also, can you send us the output of ls -l
> on the
> > wm.mgz? And finally, you probably want to use rh.aparc.annot not
> > lh.aparc.annot since you specified rh on the command line
> >
> > cheers
> > Bruce
> >
> >
> > On Fri, 24 Aug 2018, Davide Momi wrote:
> >
> > >
> > > External Email - Use Caution
> > >
> > > Dear Bruce,
> > >
> > > thanks for your response.
> > >
> > > my SUBJECTS_DIR is set to:
> /Users/davidemomi/Downloads/Broad_60_AV, which is actually
> > where the
> > > output of recon-all is located.
> > >
> > > the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory
> > >
> > > Thanks again
> > >
> > >
> > >
> > >
> > > Il giorno ven 24 ago 2018 alle ore 16:49 Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> ha
> > scritto:
> > > Hi Davide
> > >
> > > does that file exist? What is your SUBJECTS_DIR set to?
> > >
> > > cheers
> > > Bruce
> > > On Fri, 24 Aug 2018,
> > > Davide Momi wrote:
> > >
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Dear FreeSurfer,
> > > >
> > > > I have a problem when I use mris_anatomical_stats. It
> gives me an error saying
> > that it
> > > couldn't read
> > > > the input volume which is the wm.mgz file.
> > > > would you please help me how I should fix this problem?
> > > > this is the command which I used:
> > > >
> > > > mris_anatomical_stats -a label/lh.aparc.annot -b 60_AV rh
> > > >
> > > > computing statistics for each annotation in
> label/lh.aparc.annot.
> > > >
> > > > reading volume
> /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz...
> > > >
> > > >
> mghRead(/Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz, -1):
> could
> > not open
> > > file
> > > >
> > > > mris_anatomical_stats: could not read input volume
> > > > /Users/davidemomi/Downloads/Broad_60_AV//60_AV/mri/wm.mgz
> > > >
> > > >
> > > > Thanks in advance
> > > >
> > > >
> > > > Davide
> > > >
> > > >_______________________________________________
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> > > Freesurfer@nmr.mgh.harvard.edu
> > >
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> > >
> > >
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