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
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