Hello Bruce,

I am trying to check the output of the mri data that I processed I start using MNE. I placed the file in a folder called Practice in my documents, and I am using the following command:
tcsh
source your_freesurfer_dir/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR
and then
freeview -v \
good_output/mri/T1.mgz \
good_output/mri/wm.mgz \
good_output/mri/brainmask.mgz \
good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f good_output/surf/lh.white:edgecolor=blue \
good_output/surf/lh.pial:edgecolor=red \
good_output/surf/rh.white:edgecolor=blue \
good_output/surf/rh.pial:edgecolor=red
e
file
2014-08-01 19:53:06.207 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file
No such file or directory
MRISread failed
MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file
e
file
2014-08-01 19:53:07.387 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file
No such file or directory
MRISread failed
MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file

e

Do you know what is going on here?

On Jul 31, 2014, at 10:38 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Isaiah

you should go through the tutorials on our website - they detail all this
information

cheers
Bruce


On Thu, 31 Jul 2014, Isaiah C. Smith wrote:

Yes, how do i view the files and where can I find where every has been placed

On Jul 31, 2014, at 8:26 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:

there are many, many files in many different formats (e.g. volumes in
.mgz format, surfaces in our internal format, labels, parcellations,
etc...)
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:

The files after recon-all
On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:

the format of what?
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:

Thank you,
I will go there now. But regarding the output of freesurfer, the format will be .ccd?

On Jul 30, 2014, at 7:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Isaiah

you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)

cheers
Bruce

On Thu, 31 Jul 2014, Isaiah C. Smith wrote:

Thank you so much, Bruce.  I think that I got it. Overall, I am trying to
create a source volume conduction model,  calculate the lead field matrix,
and then create a source model. My instructor said that it might be possible
to do this in Freesurfer. Sorry, I am kind of new to using the terminal.
Could you tell me how to go about doing that in this program or direct me to
the part of the sit where I can start working on next steps? Or do I need to
use another program like FieldTrip for the model? Also what will the format
of the file be after the command is finished?
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9
(thresh=-3.9)
1.074  -0.133   0.048  -2.720;
0.105   1.397  -0.148  -56.728;
-0.031   0.191   1.157  -52.936;
0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9
(thresh=-3.9)
1.076  -0.124   0.028  -1.627;
0.096   1.401  -0.129  -58.732;
-0.015   0.165   1.156  -51.529;
0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
On Jul 29, 2014, at 9:24 PM, Isaiah Smith <Isaiah.C.Smith.17@dartmouth.edu>
wrote:

  The recon-all option is no longer working and neither is the
  other one. I am getting an error.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help
ERROR: Flag help unrecognized.
help
Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0:
Tue Jun  3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64
x86_64
recon-all -s  exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014
For more details, see the log file
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Isaiahs-MacBook-Pro:~ IsaiahSmith$
On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:

  Hi Isaiah

  recon-all -i <input file> -s <subject identifier> -sd <dir
  to put subject in> -all

  should  do the trick. <input file> should be  a *single*
  file in the right dicom series, or a .nii file. Don't use
  analyze
  Bruce

  On Tue, 22 Jul 2014, Isaiah C. Smith wrote:

        Hello Bruce,
        Thanks for the response; I tried the inputs
        from the check freesurfer page.
        I just tried to do the run recon-all and got
        the list of possible commands.
        The input images are unix executable files
        separately, but I can convert
        them to .hdr/.img or .nii using mricron. They
        are MRI images. How do I
        direct these files to the command? And this is
        the command to do the things
        I previously asked, right?
        Isaiah

             Hi Isaiah,

             what are the input images that you have?
        What format and what
             imaging
             sequence? You should be able to just run
        recon-all on them
             (check out
             recon-all -help)

             cheers
             Bruce
             On Tue, 22 Jul 2014, Isaiah C. Smith
        wrote:

                   Hello All,

                   I was testing to see if the
        freesurfer program works
                   and it does seem to work for
        anything besides the
                   free viewer program. I do not know
        what is wrong
                   with the others; do you have any
        ideas? Also I am
                   trying to use the inhomogeneity
        correction, convert
                   the images that I have to 1x1x1
        ratio, arrange the
                   directions of the image, and save
        the program in
                   analyze format. If possible could
        you outline that
                   process or give me a link that will
        direct me on the
                   process? Thank you. Your help is
        really appreciated.

                   Isaiah Smith
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