External Email - Use Caution Hi again Doug
FYI have sent the files as requested James ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> Sent: 08 November 2018 15:01 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume Not sure what is going on. Can you send me the input rh.area file as well as lh.40tvs8ref_sym_20.sphere.reg and 40tvs8ref_sym_20/surf/lh.sphere.reg? You can post them here https://gate.nmr.mgh.harvard.edu/filedrop2 When it asks you for an email, use gr...@nmr.mgh.harvard.edu and not my email above On 11/08/2018 08:21 AM, James Michael Roe wrote: > External Email - Use Caution > > Hi Doug > > Here is the output file > > > James Michael Roe > PhD. Candidate > Center for Lifespan Changes in Brain and Cognition > Department of Psychology > University of Oslo > PB 1094 Blindern > 0317 Oslo > Mobile: 958 49 437 > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu> > Sent: 07 November 2018 19:02 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume > > Can you send the terminal output that includes the error? > > On 11/06/2018 06:36 PM, James Michael Roe wrote: >> External Email - Use Caution >> >> Hi Bruce >> >> I realise that my last message made it sound as though the problem was fixed. >> However, I was only confirming that the files load fine in freeview (are not >> corrupted) as asked. >> The issue of many subs area and volume files failing to register when using >> --jac is still unsolved >> >> Appreciate the support. >> >> Thanks >> >> James >> >> ________________________________________ >> From: James Michael Roe >> Sent: 31 October 2018 19:45 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume >> >> Hi Bruce >> >> Can confirm that both files (rh.area & rh.volume) load fine in freeview >> >> Thanks for the help! >> >> James >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> Sent: 29 October 2018 15:43 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume >> >> Hi James >> >> can you verify that the various files (e.g. >> /cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area) >> >> are intact by loading them into freeview? For the area file you will of >> course have to load it as an overlay not as a surface (since it isn't a >> surface) >> >> cheers >> Bruce >> On Mon, 29 Oct 2018, James Michael Roe wrote: >> >>> External Email - Use Caution >>> >>> >>> Dear freesurfer experts >>> >>> >>> >>> I’m running the following commands to register RH area and volume files per >>> sub to both hemispheres >>> of a symmetrical template following Xhemi routines. >>> >>> The commands have already worked for many subs, but are failing to write >>> the target file for a >>> number of others (and all run fine without the –-jac flag) >>> >>> >>> #right to left >>> >>> mris_apply_reg \ >>> >>> --src $SUBJECTS_DIR/$sub/surf/rh.area \ >>> >>> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \ >>> >>> --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg >>> $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \ >>> >>> --jac >>> >>> >>> >>> #right to right >>> >>> mris_apply_reg \ >>> >>> --src $SUBJECTS_DIR/$sub/surf/rh.area \ >>> >>> --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \ >>> >>> --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg >>> $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \ >>> >>> --jac >>> >>> >>> >>> >>> The error is not template-specific as the output is the same using >>> fsaverage_sym >>> >>> Attached is the log file. >>> >>> >>> >>> Thanks in advance! >>> >>> >>> >>> >>> - James >>> >>> >> _______________________________________________ >> 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
