Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

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  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  > 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 > > 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 > > wrote:
>> How did you put the data on your drive?
>> 
>>> On Aug 10, 2017, at 9:25 AM, Z Hessam >> > 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 >> > 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 > 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 > 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  > 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  > 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 
>> > 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, 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

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 
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  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 
> wrote:
>
>> How did you put the data on your drive?
>>
>> On Aug 10, 2017, at 9:25 AM, Z Hessam  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 > > 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  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 <
>>> rpw...@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  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 <
 rpw...@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 <
> fis...@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 <
>>> fis...@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,
>>>   

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

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  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  > wrote:
> How did you put the data on your drive?
> 
>> On Aug 10, 2017, at 9:25 AM, Z Hessam > > 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 > > 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 >> > 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 >> > 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 > 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 > 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  > 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  >
> 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,
> 
> 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

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 
wrote:

> How did you put the data on your drive?
>
> On Aug 10, 2017, at 9:25 AM, Z Hessam  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 
> 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  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 > > 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  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 <
>>> rpw...@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 <
 fis...@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 <
>> fis...@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 \
>>
>> 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

How did you put the data on your drive?

> On Aug 10, 2017, at 9:25 AM, Z Hessam  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  > 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 > > 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 > > 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 >> > 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 >> > 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 > 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 >
 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 ",
 mri_read(): couldn't determine type of file
 
 MRIread failed: Unable to read from 
 mri_read(): couldn't determine type of file
 
 but i can load wm.mgz 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

I didn't copy the file, and drive has 3.7GB free space

On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang 
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  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 
> 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  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 > > 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 <
>>> fis...@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 <
> fis...@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 ",
> mri_read(): couldn't determine type of file
> 
> MRIread failed: Unable to read from 
> mri_read(): couldn't determine type of file
> 
> 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, 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

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  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  > 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 > > 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 > > 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 >> > 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 >> >
>>> 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 ",
>>> mri_read(): couldn't determine type of file
>>> 
>>> MRIread failed: Unable to read from 
>>> mri_read(): couldn't determine type of file
>>> 
>>> 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
>>> 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

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 
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  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 
> 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  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 > > 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 <
>>> fis...@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 <
> fis...@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 ",
> mri_read(): couldn't determine type of file
> 
> MRIread failed: Unable to read from 
> mri_read(): couldn't determine type of file
> 
> but i can load wm.mgz and other existed files in
> GUI.
>
> please help me to know why this error happend? and
> what should 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

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  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  > 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 > > 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 > > 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 >> > 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 >> >
>>> 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 ",
>>> mri_read(): couldn't determine type of file
>>> 
>>> MRIread failed: Unable to read from 
>>> mri_read(): couldn't determine type of file
>>> 
>>> 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
>>> 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

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 
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  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 
> 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 > > 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 <
 fis...@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 ",
 mri_read(): couldn't determine type of file
 
 MRIread failed: Unable to read from 
 mri_read(): couldn't determine type of file
 
 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
  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 \


 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

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  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  > 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 > > 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 > >
>> 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 ",
>> mri_read(): couldn't determine type of file
>> 
>> MRIread failed: Unable to read from 
>> mri_read(): couldn't determine type of file
>> 
>> 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
>> > 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 \
>> 
>>   

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

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 
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 
> 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 >> >
>>> 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 ",
>>> mri_read(): couldn't determine type of file
>>> 
>>> MRIread failed: Unable to read from 
>>> mri_read(): couldn't determine type of file
>>> 
>>> 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
>>>  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 ", 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 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

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 
> 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
>
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 ",
mri_read(): couldn't determine type of file

MRIread failed: Unable to read from 
mri_read(): couldn't determine type of file

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
>
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 ", 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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The information in this e-mail is intended only for the person
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it is
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and the
e-mail
contains patient information, please contact the Partners
Compliance
HelpLine at

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

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 
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 
>> 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 ",
>> mri_read(): couldn't determine type of file
>> 
>> MRIread failed: Unable to read from 
>> mri_read(): couldn't determine type of file
>> 
>> 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
>>  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 ", 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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> 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 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Bruce Fischl]

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 
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 ",
mri_read(): couldn't determine type of file

MRIread failed: Unable to read from 
mri_read(): couldn't determine type of file

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
 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 ", 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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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

$>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 
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 ",
>> mri_read(): couldn't determine type of file 
>> MRIread failed: Unable to read from  mri_read(): couldn't
>> determine type of file 
>> 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  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 ", 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
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> 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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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Bruce Fischl]

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 ",
mri_read(): couldn't determine type of file 
MRIread failed: Unable to read from  
mri_read(): couldn't determine type of file 

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  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 ", 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.

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

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 ",

mri_read(): couldn't determine type of file 
MRIread failed: Unable to read from 
mri_read(): couldn't determine type of file 

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  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 ", 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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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.