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.hes...@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 <rpw...@nmr.mgh.harvard.edu 
> <mailto:rpw...@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.hes...@gmail.com 
>> <mailto:z.hes...@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 <rpw...@nmr.mgh.harvard.edu 
>> <mailto:rpw...@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.hes...@gmail.com 
>>> <mailto:z.hes...@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 <rpw...@nmr.mgh.harvard.edu 
>>> <mailto:rpw...@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.hes...@gmail.com 
>>>> <mailto:z.hes...@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 <rpw...@nmr.mgh.harvard.edu 
>>>> <mailto:rpw...@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.hes...@gmail.com 
>>>>> <mailto:z.hes...@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 <rpw...@nmr.mgh.harvard.edu 
>>>>> <mailto: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 <mailto: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 
>>>>>> <mailto: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 <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.hes...@gmail.com <mailto:z.hes...@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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>>>>>> The information in this e-mail is intended only for the person to whom
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>>>>> 
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>>>>> The information in this e-mail is intended only for the person to whom it 
>>>>> is
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>>>>> but does not contain patient information, please contact the sender and 
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>>>> 
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>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
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