Thanks Sent from my iPhone
> On Jul 31, 2014, at 10:47 AM, "Bruce Fischl" <fis...@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" <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 > _______________________________________________ > 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
