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" <fis...@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" <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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
