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?
Best Regards, Mahtab.
Hi Mahtab
can you please send the screen output of the command you ran and what it printed, and also what the environment variable SUBJECTS_DIR is?
cheers Bruce On Thu, 19 May 2016, Mahtab Farahbakhsh wrote:
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?
Best Regards, Mahtab.
Dear Bruce,
This is the input command and the output that I get:
bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz
or:
mris_anatomical_stats -l anon/label/lh.BA45.label anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz
This is the SUBJECTS_DIR
export SUBJECTS_DIR=/Applications/freesurfer/experimental_data/TG/anon
cd $SUBJECTS_DIR Best Regards, Mahtab.
On 19 May 2016 at 13:41, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mahtab
can you please send the screen output of the command you ran and what it printed, and also what the environment variable SUBJECTS_DIR is?
cheers Bruce
On Thu, 19 May 2016, Mahtab Farahbakhsh wrote:
Dear FreeSurfer,
I have a problem when I use mris_anatomical_stats. It gives me an error saying that it couldn't read the input volume which is the wm.mgz file. would you please help me how I should fix this problem?
Best Regards, Mahtab.
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The second one is a valid command (1st is not). What is the full path to the wm.mgz file that is in your anlayzed data?
On 05/19/2016 10:33 AM, Mahtab Farahbakhsh wrote:
Dear Bruce,
This is the input command and the output that I get:
bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz
or:
mris_anatomical_stats -l anon/label/lh.BA45.label anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz
This is the SUBJECTS_DIR
export SUBJECTS_DIR=/Applications/freesurfer/experimental_data/TG/anon
cd $SUBJECTS_DIR
Best Regards, Mahtab.
On 19 May 2016 at 13:41, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Mahtab can you please send the screen output of the command you ran and what it printed, and also what the environment variable SUBJECTS_DIR is? cheers Bruce On Thu, 19 May 2016, Mahtab Farahbakhsh wrote: Dear FreeSurfer, I have a problem when I use mris_anatomical_stats. It gives me an error saying that it couldn't read the input volume which is the wm.mgz file. would you please help me how I should fix this problem? Best Regards, Mahtab. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Dear Douglas,
The wm.mgz is in the mri folder so it's in:
Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz.
Best Regards, Mahtab.
Sent from myMail for iOS
Thursday, May 19, 2016, 16:19 +0100 from greve@nmr.mgh.harvard.edu greve@nmr.mgh.harvard.edu:
The second one is a valid command (1st is not). What is the full path to the wm.mgz file that is in your anlayzed data?
On 05/19/2016 10:33 AM, Mahtab Farahbakhsh wrote:
Dear Bruce,
This is the input command and the output that I get:
bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz
or:
mris_anatomical_stats -l anon/label/lh.BA45.label anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz
This is the SUBJECTS_DIR
export SUBJECTS_DIR=/Applications/freesurfer/experimental_data/TG/anon
cd $SUBJECTS_DIR
Best Regards, Mahtab.
On 19 May 2016 at 13:41, Bruce Fischl < fischl@nmr.mgh.harvard.edu <mailto: fischl@nmr.mgh.harvard.edu >> wrote:
Hi Mahtab can you please send the screen output of the command you ran and what it printed, and also what the environment variable SUBJECTS_DIR is? cheers Bruce On Thu, 19 May 2016, Mahtab Farahbakhsh wrote: Dear FreeSurfer, I have a problem when I use mris_anatomical_stats. It gives me an error saying that it couldn't read the input volume which is the wm.mgz file. would you please help me how I should fix this problem? Best Regards, Mahtab. _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu <mailto: Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Hi Mahtab
the mris_anatomical_stats help says:
mris_anatomical_stats [options] <subjectname> <hemi> [<surfacename>] . . . -f <tablefile> table output to tablefile (different format than -b). Must use-a or -l options to spec input. . . .
so you are specifycing the name of the table as "anon", the name of the subject as "lh", the name of the hemi as "anon" and the surface name as "lh".
On Thu, 19 May 2016, Mahtab Farahbakhsh wrote:
Dear Bruce, This is the input command and the output that I get:
bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz
or:
mris_anatomical_stats -l anon/label/lh.BA45.label anon lh limiting computations to label anon/label/lh.BA45.label. reading volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz... mghRead(/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz, -1): could not open file mris_anatomical_stats: could not read input volume /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz
This is the SUBJECTS_DIR
export SUBJECTS_DIR=/Applications/freesurfer/experimental_data/TG/anon
cd $SUBJECTS_DIR
Best Regards, Mahtab.
On 19 May 2016 at 13:41, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mahtab
can you please send the screen output of the command you ran and what it printed, and also what the environment variable SUBJECTS_DIR is? cheers Bruce On Thu, 19 May 2016, Mahtab Farahbakhsh wrote: 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? Best Regards, Mahtab.
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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.
please send the command line and all terminal output
On 05/19/2016 05:50 AM, Mahtab Farahbakhsh wrote:
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?
Best Regards, Mahtab.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Mahtab Farahbakhsh