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" <fis...@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 <fis...@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...@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 <fis...@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 >>>>> _______________________________________________ >>>>> 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. >>>>> >>>>> _______________________________________________ >>>>> 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 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 > > _______________________________________________ > 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
