Hello Freesurfer Developers,
I have problem when I use "freeview" example code in terminal,
freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red
it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI.
please help me to know why this error happend? and what should I do to solve this?
I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please
regards
Hello Freesurfer Developers,
I have problem when I use "freeview" example code in terminal,
freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red
it tell "Failed to load MRI <subject_dir>",
mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir>
but i can load wm.mgz and other existed files in GUI.
please help me to know why this error happend? and what should I do to solve this?
I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please
regards
On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam z.hessam@gmail.com wrote:
Hello Freesurfer Developers,
I have problem when I use "freeview" example code in terminal,
freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red
it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI.
please help me to know why this error happend? and what should I do to solve this?
I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please
regards
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview?
On Wed, 9 Aug 2017, Z Hessam wrote:
Hello Freesurfer Developers,
I have problem when I use "freeview" example code in terminal, freeview -v \
bert/mri/T1.mgz \
bert/mri/wm.mgz \
bert/mri/brainmask.mgz \
bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f \
bert/surf/lh.white:edgecolor=blue \
bert/surf/lh.pial:edgecolor=red \
bert/surf/rh.white:edgecolor=blue \
bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI.
please help me to know why this error happend? and what should I do to solve this?
I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please
regards
On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam z.hessam@gmail.com wrote:
Hello Freesurfer Developers,
I have problem when I use "freeview" example code in terminal, freeview -v \
bert/mri/T1.mgz \
bert/mri/wm.mgz \
bert/mri/brainmask.mgz \
bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f \
bert/surf/lh.white:edgecolor=blue \
bert/surf/lh.pial:edgecolor=red \
bert/surf/rh.white:edgecolor=blue \
bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI.
please help me to know why this error happend? and what should I do to solve this?
I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please
regards
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview?
On Wed, 9 Aug 2017, Z Hessam wrote:
Hello Freesurfer Developers,
I have problem when I use "freeview" example code in terminal, freeview -v \
bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=redit tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI.
please help me to know why this error happend? and what should I do to solve this?
I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please
regards
On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam z.hessam@gmail.com wrote:
Hello Freesurfer Developers,
I have problem when I use "freeview" example code in terminal, freeview -v \
bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=redit tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI.
please help me to know why this error happend? and what should I do to solve this?
I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please
regards
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.
can you try it without all the \ characters? You shouldn't need them if it's all on one line On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
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.
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
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.
Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
can you try it without all the \ characters? You shouldn't need them if it's all on one line On Wed, 9 Aug 2017, Z Hessam wrote: $>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ I use the example 4 in the "download and install" page of site On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com <mailto:z.hessam@gmail.com>> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam z.hessam@gmail.com wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com <mailto:z.hessam@gmail.com>> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 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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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 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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it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/ subjects/bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam z.hessam@gmail.com wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/ freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/ freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
What if you run:
freeview -v /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
On Aug 10, 2017, at 4:40 AM, Z Hessam z.hessam@gmail.com wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com <mailto:z.hessam@gmail.com>> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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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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 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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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 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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again that error, it shows:
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
On Thu, Aug 10, 2017 at 5:19 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
What if you run:
freeview -v /media/hessam91/driver2/freesurfer/freesurfer/ subjects/bert/mri/T1.mgz
On Aug 10, 2017, at 4:40 AM, Z Hessam z.hessam@gmail.com wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/ freesurfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/ bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam z.hessam@gmail.com wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu
wrote:
Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Wait, the file size looks too small. Only 1590 bytes. Did the data get copied properly? Is your drive full?
On Aug 10, 2017, at 4:40 AM, Z Hessam z.hessam@gmail.com wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com <mailto:z.hessam@gmail.com>> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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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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 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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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 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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I didn't copy the file, and drive has 3.7GB free space
On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
Wait, the file size looks too small. Only 1590 bytes. Did the data get copied properly? Is your drive full?
On Aug 10, 2017, at 4:40 AM, Z Hessam z.hessam@gmail.com wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/ freesurfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/ bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam z.hessam@gmail.com wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu
wrote:
Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
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.
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
How did you put the data on your drive?
On Aug 10, 2017, at 9:25 AM, Z Hessam z.hessam@gmail.com wrote:
I didn't copy the file, and drive has 3.7GB free space
On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Wait, the file size looks too small. Only 1590 bytes. Did the data get copied properly? Is your drive full?
On Aug 10, 2017, at 4:40 AM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com <mailto:z.hessam@gmail.com>> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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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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 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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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 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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I copy the *.tar.gz file, and open and install the program by terminal. I am confused because that work last week for this data, but now, this doesn't work. for other datasets, i copy dicom files, then convert them with " recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid fat_fh23" command to *.mgz, and then i use the "recon-all -s .... -all " command in linux terminal.
On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
How did you put the data on your drive?
On Aug 10, 2017, at 9:25 AM, Z Hessam z.hessam@gmail.com wrote:
I didn't copy the file, and drive has 3.7GB free space
On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
Wait, the file size looks too small. Only 1590 bytes. Did the data get copied properly? Is your drive full?
On Aug 10, 2017, at 4:40 AM, Z Hessam z.hessam@gmail.com wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu
wrote:
Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/be rt/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam z.hessam@gmail.com wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang < rpwang@nmr.mgh.harvard.edu> wrote:
Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut :opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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OK. Actually I was wrong, the file has size of 0! I don’t know what happened when you installed freesurfer or ran recon-all, but the file was not properly written...
On Aug 10, 2017, at 9:34 AM, Z Hessam z.hessam@gmail.com wrote:
I copy the *.tar.gz file, and open and install the program by terminal. I am confused because that work last week for this data, but now, this doesn't work. for other datasets, i copy dicom files, then convert them with " recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid fat_fh23" command to *.mgz, and then i use the "recon-all -s .... -all " command in linux terminal.
On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: How did you put the data on your drive?
On Aug 10, 2017, at 9:25 AM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
I didn't copy the file, and drive has 3.7GB free space
On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Wait, the file size looks too small. Only 1590 bytes. Did the data get copied properly? Is your drive full?
On Aug 10, 2017, at 4:40 AM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com <mailto:z.hessam@gmail.com>> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
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it seems that I should run it again thank you for your helps best regards
On Thu, Aug 10, 2017 at 6:27 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
OK. Actually I was wrong, the file has size of 0! I don’t know what happened when you installed freesurfer or ran recon-all, but the file was not properly written...
On Aug 10, 2017, at 9:34 AM, Z Hessam z.hessam@gmail.com wrote:
I copy the *.tar.gz file, and open and install the program by terminal. I am confused because that work last week for this data, but now, this doesn't work. for other datasets, i copy dicom files, then convert them with " recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid fat_fh23" command to *.mgz, and then i use the "recon-all -s .... -all " command in linux terminal.
On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
How did you put the data on your drive?
On Aug 10, 2017, at 9:25 AM, Z Hessam z.hessam@gmail.com wrote:
I didn't copy the file, and drive has 3.7GB free space
On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu
wrote:
Wait, the file size looks too small. Only 1590 bytes. Did the data get copied properly? Is your drive full?
On Aug 10, 2017, at 4:40 AM, Z Hessam z.hessam@gmail.com wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang < rpwang@nmr.mgh.harvard.edu> wrote:
Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/be rt/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam z.hessam@gmail.com wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang < rpwang@nmr.mgh.harvard.edu> wrote:
Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
> $>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ > bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut > :opacity=0.2 > mri_read(): couldn't determine type of file > /media/hessam91/driver2/freesurfer/freesurfer/subjects/ > MRIread failed: Unable to read from > /media/hessam91/driver2/freesurfer/freesurfer/subjects/ > mri_read(): couldn't determine type of file > /media/hessam91/driver2/freesurfer/freesurfer/subjects/ > > > I use the example 4 in the "download and install" page of site > > On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl < > fischl@nmr.mgh.harvard.edu> > wrote: > > hmmm, that looks ok, but it's hard to tell with all the > backslashes and blank lines and such. Can you send the full > command on a single line (e.g. by hitting up-arrow in the > terminal window) and the actual output of freeview? > > On Wed, 9 Aug 2017, Z Hessam wrote: > > > Hello Freesurfer Developers, > > I have problem when I use "freeview" example code in > terminal, > freeview -v \ > > bert/mri/T1.mgz \ > > bert/mri/wm.mgz \ > > bert/mri/brainmask.mgz \ > > > bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ > > -f \ > > bert/surf/lh.white:edgecolor=blue \ > > bert/surf/lh.pial:edgecolor=red \ > > bert/surf/rh.white:edgecolor=blue \ > > bert/surf/rh.pial:edgecolor=red > it tell "Failed to load MRI <subject_dir>", > mri_read(): couldn't determine type of file > <subject_dir> > MRIread failed: Unable to read from <subject_dir> > mri_read(): couldn't determine type of file > <subject_dir> > but i can load wm.mgz and other existed files in > GUI. > > please help me to know why this error happend? and > what should I do to solve > this? > > I've searched the list, I found a similar errors, > but wasn't helpful answer reported. > help me please > > regards > > On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam > z.hessam@gmail.com wrote: > > Hello Freesurfer Developers, > > I have problem when I use "freeview" example code in > terminal, > freeview > -v \ > > bert/mri/T1.mgz \ > > bert/mri/wm.mgz \ > > bert/mri/brainmask.mgz \ > > > bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ > > -f \ > > bert/surf/lh.white:edgecolor=blue \ > > bert/surf/lh.pial:edgecolor=red \ > > bert/surf/rh.white:edgecolor=blue \ > > bert/surf/rh.pial:edgecolor=red > it tell "Failed to load MRI <subject_dir>", but i > can load wm.mgz and other existed files in GUI. > > please help me to know why this error happend? and > what should I do to solve > this? > > I've searched the list, I found a similar errors, > but wasn't helpful answer reported. > help me please > > regards > > > > > _______________________________________________ > 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
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Sure. Please make sure you have as much as spare disk space as you can.
On Aug 10, 2017, at 4:12 PM, Z Hessam z.hessam@gmail.com wrote:
it seems that I should run it again thank you for your helps best regards
On Thu, Aug 10, 2017 at 6:27 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: OK. Actually I was wrong, the file has size of 0! I don’t know what happened when you installed freesurfer or ran recon-all, but the file was not properly written...
On Aug 10, 2017, at 9:34 AM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
I copy the *.tar.gz file, and open and install the program by terminal. I am confused because that work last week for this data, but now, this doesn't work. for other datasets, i copy dicom files, then convert them with " recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid fat_fh23" command to *.mgz, and then i use the "recon-all -s .... -all " command in linux terminal.
On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: How did you put the data on your drive?
On Aug 10, 2017, at 9:25 AM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
I didn't copy the file, and drive has 3.7GB free space
On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Wait, the file size looks too small. Only 1590 bytes. Did the data get copied properly? Is your drive full?
On Aug 10, 2017, at 4:40 AM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam <z.hessam@gmail.com mailto:z.hessam@gmail.com> wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com <mailto:z.hessam@gmail.com>> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Ruopeng Wang -
Z Hessam