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 > <bfis...@mgh.harvard.edu> 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: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Angela Favaro > Sent: Sunday, June 28, 2020 8:03 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > 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 > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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