Hi Ritesh you need to give us much more information if we are to be able to help you. We need the exact command you ran, the full screen output of the command, and the contents of the subjects recon-all.log file in <subject>/scripts/recon-all.log
cheers Bruce On Fri, 11 May 2018, Ritesh Mahajan wrote: > External Email - Use Caution > > Hello Bruce, > > 1) I converted the my mri data from ALS to RAI orientation through command > "mri_convert --out_orientation RAI inputALS.nii outputRAI.nii" > 2) Then i gave a run for free-surfer, using recon-all command. After > successful run of free-surfer without any error message, still i do not see > any results generated by free-surfer. Any you please help why is it so ? > 3) Under results mri folder i see only orig.mgz, orig_nu.mgz and rawavg.mgz. > Other results are not generated. > > Please can you explain why this happening ? > > Thanks, > Ritesh Mahajan > > ----- Original Message ----- > From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> > Sent: Thursday, May 10, 2018 9:50:44 PM > Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and > dimension > > because internally we expect things to be a certain way (which is why we > convert the data to that format). There are also some requirements on the > data that you have to meet. For example 2mm is not high enough resolution > to get accurate cortical models. The acquired data has to be no bigger than > about 1.5mm in any dimension. > > cheers > Bruce > > > On Thu, 10 May 2018, Ritesh Mahajan wrote: > >> External Email - Use Caution >> >> Hi Bruce, >> >> Thanks Bruce i understand that. >> >> But can't i run free-surfer with all these parameters (size, spacing and >> orientation) ? >> >> Thanks, >> Ritesh Mahajan >> >> ----- Original Message ----- >> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >> To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >> Sent: Thursday, May 10, 2018 8:22:38 PM >> Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and >> dimension >> >> Hi Ritesh >> >> your best bet is to run everything normally, then convert the output to >> whatever format/orientation/voxel size you want >> >> cheers >> Bruce >> On Thu, 10 May 2018, Ritesh >> Mahajan wrote: >> >>> External Email - Use Caution >>> >>> Thank you Bruse. Actually i converted the input into RAI orientation using >>> mri_convert --out_orientation and gave RAI input the free-surfer through >>> recon-all. The results are not generated. >>> >>> My goal is to run free-surfer with RAI orientation and result should be in >>> RAI. I also want the output of free-surfer with dimensions as 128*128*128 >>> and spacing as 2,2,2 mm. >>> >>> Can you tell whether this can be done using free-surfer? >>> >>> Thanks, >>> Ritesh Mahajan >>> >>> ----- Original Message ----- >>> From: "Ritesh Mahajan" <ritesh.maha...@ripl.ricoh.com> >>> To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >>> Sent: Thursday, May 10, 2018 1:44:40 PM >>> Subject: run recon all with forced orientation, spacing and dimension >>> >>> External Email - Use Caution >>> >>> Hello Team, >>> >>> As i know free-surfer generates the output with following: >>> 1) Dimensions : 256*256*256 >>> 2) Spacing : 1, 1,1 mm >>> 3) Orientation : LIA >>> >>> Is there any way to run free-surfer with user specified orientation, >>> spacing and dimension ? >>> >>> Thanks, >>> Ritesh Mahajan >>> >>> _______________________________________________ >>> 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
