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.edumailto: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.edumailto: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.edumailto: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.edumailto: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.edumailto: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.
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