External Email - Use Caution For this dataset, I named cases 001.mgz 002.mgz ... and controls 101.mgz 102.mgz...
But the error message also appear when I rename that volume... Ottieni BlueMail per Android Il giorno 28 giu 2020, 20:46, alle ore 20:46, "Fischl, Bruce" <[email protected]> ha scritto: >Are you sure 102.mgz is from our analysis previously? We typically name >the volumes 001.mgz, 002.mgz, etc.... > >From: [email protected] ><[email protected]> On Behalf Of Angela Favaro >Sent: Sunday, June 28, 2020 1:49 PM >To: Freesurfer support list <[email protected]> >Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames! > > > External Email - Use Caution >Sure! >thank you for any help! >Angela > >angelafavaro% recon-all -all -s subj102 >Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b >Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b >INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen >Actual FREESURFER_HOME /Applications/freesurfer/7.1.0 >-rw-rw-r-- 1 angelafavaro staff 143379 Jun 28 13:46 >/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log >Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 >16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64 >#-------------------------------------------- >#@# MotionCor Sun Jun 28 19:40:10 CEST 2020 >Found 1 runs >/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz >Checking for (invalid) multi-frame inputs... >ERROR: input(s) cannot have multiple frames! >/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has frames >Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 >16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64 > >recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST >2020 > >For more details, see the log file >/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log >To report a problem, see >http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >Then I copied 102.mgz in a different folder. I also copied in this >folder the files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz >from a previous (successful) analysis with Freesurfer 6.0 > >angelafavaro% mri_info 102.mgz >mri_info(77526,0x11d011dc0) malloc: can't allocate region >*** mach_vm_map(size=8386104309919531008) failed (error code=3) >mri_info(77526,0x11d011dc0) malloc: *** set a breakpoint in >malloc_error_break to debug >error: Cannot allocate memory >error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes! > >angelafavaro% mri_info 1023.mgz >mri_info(77711,0x1125ffdc0) malloc: can't allocate region >*** mach_vm_map(size=8386104309919531008) failed (error code=3) >mri_info(77711,0x1125ffdc0) malloc: *** set a breakpoint in >malloc_error_break to debug >error: Cannot allocate memory >error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes! > >mri_info rawavg.mgz >mri_info(77716,0x11438bdc0) malloc: can't allocate region >*** mach_vm_map(size=8386104309919531008) failed (error code=3) >mri_info(77716,0x11438bdc0) malloc: *** set a breakpoint in >malloc_error_break to debug >error: Cannot allocate memory >error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes! > > >mri_info orig.mgz >Volume information for orig.mgz > type: MGH > dimensions: 256 x 256 x 256 > voxel sizes: 1.000000, 1.000000, 1.000000 > type: UCHAR (0) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 >TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 >degrees > nframes: 1 > PhEncDir: UNKNOWN > FieldStrength: 0.000000 >ras xform present >xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = >-2.5219 > : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 10.8637 > : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = -32.3759 > >talairach xfm : >/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm >Orientation : LIA >Primary Slice Direction: coronal > >voxel to ras transform: > -1.0000 0.0000 -0.0000 125.4781 > 0.0000 -0.0000 1.0000 -117.1363 > -0.0000 -1.0000 -0.0000 95.6241 > 0.0000 0.0000 0.0000 1.0000 > >voxel-to-ras determinant -1 > >ras to voxel transform: > -1.0000 -0.0000 -0.0000 125.4781 > 0.0000 -0.0000 -1.0000 95.6241 > 0.0000 1.0000 -0.0000 117.1363 > -0.0000 -0.0000 -0.0000 1.0000 > > > > > > >Il giorno 28 giu 2020, alle ore 17:51, Fischl, Bruce ><[email protected]<mailto:[email protected]>> ha scritto: > >HI Angela > >Can you send us the complete command line and screen output of the >commands you ran that worked and the ones that failed? > >Cheers >Bruce > >From: >[email protected]<mailto:[email protected]> ><[email protected]<mailto:[email protected]>> >On Behalf Of Angela Favaro >Sent: Sunday, June 28, 2020 8:03 AM >To: Freesurfer support list ><[email protected]<mailto:[email protected]>> >Subject: [Freesurfer] ERROR: input(s) cannot have multiple frames! > > External Email - Use Caution >Dear Freesurfer experts, >I have a problem with a T1 volume of my dataset and I am not able to >understand it. >This volume was correctly analyzed by Freesurfer 6. >Whan I run recon-all with Freesurfer 7.1 the following error appear: > >Checking for (invalid) multi-frame inputs... >ERROR: input(s) cannot have multiple frames! >/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has frames >Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 >16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64 > >recon-all -s subj102 exited with ERRORS at Sun Jun 28 13:46:17 CEST >2020 > > > > > > > > > >Using Freeview I was not able to see the volume and when I tried, as >suggested in the support list, to run mri_info: > > > > > > >mri_info(21013,0x11e0d7dc0) malloc: can't allocate region >*** mach_vm_map(size=8386104309919531008) failed (error code=3) >mri_info(21013,0x11e0d7dc0) malloc: *** set a breakpoint in >malloc_error_break to debug >error: Cannot allocate memory >error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes! > > > > > > > > > > > > >When I tried to run mri_info with the file rawavg.mgz (from previous >analysis with Freesurfer 6) the same error message appeared (and >Freeview was not able to open it). But when I used the file orig.mgz, I >obtained the below output and Freeview was able to open the volume. But >when I tried to use the orig.mgz file as the input file (renamed >001.mgz) in the subj/mri/orig folder, again the error output appear >(ERROR: input(s) cannot have multiple frames!). What is the problem >according to you? >Thank you for any help >Angela > > > > > > >Volume information for orig.mgz > type: MGH > dimensions: 256 x 256 x 256 > voxel sizes: 1.000000, 1.000000, 1.000000 > type: UCHAR (0) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 >TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 >degrees > nframes: 1 > PhEncDir: UNKNOWN > FieldStrength: 0.000000 >ras xform present >xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = >-2.5219 > : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 10.8637 > : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = -32.3759 > >talairach xfm : >/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm >Orientation : LIA >Primary Slice Direction: coronal > >voxel to ras transform: > -1.0000 0.0000 -0.0000 125.4781 > 0.0000 -0.0000 1.0000 -117.1363 > -0.0000 -1.0000 -0.0000 95.6241 > 0.0000 0.0000 0.0000 1.0000 > >voxel-to-ras determinant -1 > >ras to voxel transform: > -1.0000 -0.0000 -0.0000 125.4781 > 0.0000 -0.0000 -1.0000 95.6241 > 0.0000 1.0000 -0.0000 117.1363 > -0.0000 -0.0000 -0.0000 1.0000 > > > > >_______________________________________________ >Freesurfer mailing list >[email protected]<mailto:[email protected]> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >------------------------------------------------------------------------ > >_______________________________________________ >Freesurfer mailing list >[email protected] >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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