Error with mris_anatomical_stats

List overview All Threads
Download

newer

older

Unable to copy the license.txt...

bbregister error

Davide Momi

24 Aug 2018 24 Aug '18

5:14 a.m.

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

Attachments:

attachment.html (text/html — 3.4 KB)

Show replies by date

Bruce Fischl

24 Aug 24 Aug

10:48 a.m.

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

Davide Momi

10:53 a.m.

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.

Bruce Fischl

11:34 a.m.

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.

Davide Momi

11:42 a.m.

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.

Bruce Fischl

12:02 p.m.

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.

Davide Momi

12:09 p.m.

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.

2839

Age (days ago)

2839

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

6 comments

2 participants

tags (0)

participants (2)

Bruce Fischl
Davide Momi