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
