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 <fischl@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 <fischl@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 <fischl@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 
>       >       >
>       >       >_______________________________________________
>       >       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
>
>
>       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


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.