External Email - Use Caution
Hello,
I was wondering if I can get some help. Every time I try to run my T1 image with a T2 FLAIR to enhance pial surfaces, I get the following message:
Computing pial target locations using multimodal (2) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.01, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=2 Creating lowres distance volumes t=0.000581909 Creating white distance volumes t=0.773706 (box.dx, box.dy, box.dz) = (118, 218, 310) (region->dx, region->dy, region->dz) = (118, 218, 310) (region->dx, region->dy, region->dz) = (118, 218, 310) Creating pial distance volumes t=1.42513 (box.dx, box.dy, box.dz) = (124, 226, 314) (region->dx, region->dy, region->dz) = (124, 226, 314) (region->dx, region->dy, region->dz) = (124, 226, 314) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 2.14683 Starting loop over 106284 vertices vno = 0, t = 2.14683 error: Cannot allocate memory error: HISTOalloc(-2147483648): could not allocate histogram
I am currently using the command
recon-all -subject <subject name> -FLAIR 106_T2w_FLAIR_AX_SENSEBrain_res.nii.gz -FLAIRpial -all -noskullstrip
The error log is attached below. I looked at filled.mgz, it does not seem to have any skull or cerebellum in it. Any help would be appreciated!
Sincerely, Pankush Kumar
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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 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
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 BFISCHL@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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 CautionDear 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
Are you sure 102.mgz is from our analysis previously? We typically name the volumes 001.mgz, 002.mgz, etc....
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Angela Favaro Sent: Sunday, June 28, 2020 1:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu 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 <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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...
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Il giorno 28 giu 2020, 20:46, alle ore 20:46, "Fischl, Bruce" bfischl@mgh.harvard.edu ha scritto:
Are you sure 102.mgz is from our analysis previously? We typically name the volumes 001.mgz, 002.mgz, etc....
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Angela Favaro Sent: Sunday, June 28, 2020 1:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!
External Email - Use CautionSure! 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 <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] ERROR: input(s) cannot have multiple frames!
External Email - Use CautionDear 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.edumailto: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
External Email - Use Caution
Yes, I am sure Now I tried to use Freesurfer 6.0 again for that volume and both recon-all and mri_info worked:
recon-all -all -s subj102 Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/prova Actual FREESURFER_HOME /Applications/freesurfer Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun 2 20:26:31 PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# MotionCor Sun Jun 28 22:44:04 CEST 2020 Found 1 runs /Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. …. …..
mri_info subj102/mri/orig/102.mgz Volume information for subj102/mri/orig/102.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 20:45, Fischl, Bruce BFISCHL@MGH.HARVARD.EDU ha scritto:
Are you sure 102.mgz is from our analysis previously? We typically name the volumes 001.mgz, 002.mgz, etc….
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Angela Favaro Sent: Sunday, June 28, 2020 1:49 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!
External Email - Use CautionSure! 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 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 <BFISCHL@MGH.HARVARD.EDU mailto:BFISCHL@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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 CautionDear 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
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
Hmmm, can you send us the volume offlist?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Angela Favaro Sent: Sunday, June 28, 2020 4:53 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!
External Email - Use Caution Yes, I am sure Now I tried to use Freesurfer 6.0 again for that volume and both recon-all and mri_info worked:
recon-all -all -s subj102 Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/prova Actual FREESURFER_HOME /Applications/freesurfer Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun 2 20:26:31 PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# MotionCor Sun Jun 28 22:44:04 CEST 2020 Found 1 runs /Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. …. …..
mri_info subj102/mri/orig/102.mgz Volume information for subj102/mri/orig/102.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 20:45, Fischl, Bruce <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> ha scritto:
Are you sure 102.mgz is from our analysis previously? We typically name the volumes 001.mgz, 002.mgz, etc….
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Angela Favaro Sent: Sunday, June 28, 2020 1:49 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> 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 <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
What is an offlist? I am running a longitudinal analysis and in the SUBJECTS directory there are now the following folders
I had this problem only with subj102 (subj102/mri/orig/102.mgz)
subj001 subj001.long.template18 subj003 subj003.long.template17 subj004 subj004.long.template16 subj005 subj006 subj006.long.template14 subj007 subj007.long.template13 subj008 subj008.long.template12 subj009 subj009.long.template11 subj010 subj010.long.template10 subj011 subj011.long.template9 subj012 subj013 subj013.long.template7 subj014 subj014.long.template6 subj015 subj015.long.template5 subj016 subj016.long.template4 subj017 subj017.long.template3 subj018 subj018.long.template2 subj019 subj019.long.template1 subj020 subj020.long.template19 subj021 subj021.long.template20 subj023 subj023.long.template21 subj024 subj027 subj027.long.template23 subj029 subj029.long.template24 subj031 subj031.long.template25 subj034 subj034.long.template27 subj035 subj035.long.template28 subj036 subj038 subj038.long.template30 subj041 subj041.long.template31 subj042 subj042.long.template32 subj043 subj043.long.template33 subj044 subj045 subj047 subj049 subj049.long.template37 subj058 subj058.long.template38 subj060 subj060.long.template39 subj101 subj101.long.template40 subj102 subj103 subj103.long.template42 subj104 subj104.long.template43 subj105 subj105.long.template44 subj106 subj106.long.template45 subj107 subj107.long.template46 subj108 subj108.long.template47 subj109 subj110 subj110.long.template49 subj111 subj112 subj112.long.template51 subj113 subj113.long.template52 subj114 subj114.long.template53 subj115 subj115.long.template54 subj116 subj116.long.template55 subj117 subj117.long.template56 subj201 subj201.long.template4 subj202 subj202.long.template2 subj203 subj203.long.template6 subj204 subj204.long.template1 subj205 subj205.long.template3 subj206 subj206.long.template5 subj207 subj207.long.template7 subj208 subj208.long.template12 subj209 subj209.long.template9 subj210 subj210.long.template10 subj211 subj212 subj212.long.template11 subj213 subj213.long.template13 subj214 subj215 subj215.long.template16 subj216 subj216.long.template14 subj217 subj217.long.template17 subj218 subj218.long.template18 subj220 subj221 subj221.long.template21 subj222 subj222.long.template19 subj224 subj224.long.template20 subj225 subj225.long.template24 subj226 subj226.long.template28 subj227 subj227.long.template25 subj229 subj229.long.template23 subj230 subj230.long.template27 subj231 subj231.long.template29 subj232 subj233 subj233.long.template32 subj234 subj235 subj235.long.template33 subj236 subj236.long.template37 subj237 subj238 subj239 subj239.long.template31 subj241 subj241.long.template38 subj242 subj242.long.template39 subj301 subj301.long.template49 subj302 subj302.long.template53 subj303 subj303.long.template44 subj304 subj304.long.template55 subj305 subj305.long.template45 subj306 subj306.long.template54 subj307 subj308 subj308.long.template42 subj309 subj309.long.template51 subj310 subj310.long.template52 subj311 subj312 subj313 subj313.long.template47 subj314 subj314.long.template46 subj315 subj315.long.template40 subj316 subj316.long.template43 subj317 subj317.long.template56 subject_list.txt subject_list_all 2.txt subject_list_long.txt subject_list_long1.txt subject_list_long2.txt subject_list_long3.txt template1 template10 template11 template12 template13 template14 template15 template16 template17 template18 template19 template2 template20 template21 template22 template23 template24 template25 template26 template27 template28 template29 template3 template30 template31 template32 template33 template34 template35 template36 template37 template38 template39 template4 template40 template41 template42 template43 template44 template45 template46 template47 template48 template49 template5 template50 template51 template52 template53 template54 template55 template56 template6 template7 template8 template9
And how did you generate the volumes? I wouldn’t name them 001.mgz, that will end up being confusing. Maybe something like sub.001.mgz might be better, since otherwise we might overwrite some of them
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Angela Favaro Sent: Sunday, June 28, 2020 4:53 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!
External Email - Use Caution Yes, I am sure Now I tried to use Freesurfer 6.0 again for that volume and both recon-all and mri_info worked:
recon-all -all -s subj102 Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/prova Actual FREESURFER_HOME /Applications/freesurfer Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun 2 20:26:31 PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# MotionCor Sun Jun 28 22:44:04 CEST 2020 Found 1 runs /Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. …. …..
mri_info subj102/mri/orig/102.mgz Volume information for subj102/mri/orig/102.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 20:45, Fischl, Bruce <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> ha scritto:
Are you sure 102.mgz is from our analysis previously? We typically name the volumes 001.mgz, 002.mgz, etc….
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Angela Favaro Sent: Sunday, June 28, 2020 1:49 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> 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 <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
How did you generate 102.mgz? It looks like it was created by a pretty old version of FS.
On 6/28/2020 5:41 PM, Fischl, Bruce wrote:
And how did you generate the volumes? I wouldn’t name them 001.mgz, that will end up being confusing. Maybe something like sub.001.mgz might be better, since otherwise we might overwrite some of them
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Angela Favaro *Sent:* Sunday, June 28, 2020 4:53 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!
* External Email - Use Caution *
Yes, I am sure
Now I tried to use Freesurfer 6.0 again for that volume and both recon-all and mri_info worked:
recon-all -all -s subj102
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/prova
Actual FREESURFER_HOME /Applications/freesurfer
Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun 2 20:26:31 PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64
#--------------------------------------------
#@# MotionCor Sun Jun 28 22:44:04 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
….
…..
mri_info subj102/mri/orig/102.mgz
Volume information for subj102/mri/orig/102.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 20:45, Fischl, Bruce <BFISCHL@MGH.HARVARD.EDU <mailto:BFISCHL@MGH.HARVARD.EDU>> ha scritto: Are you sure 102.mgz is from our analysis previously? We typically name the volumes 001.mgz, 002.mgz, etc…. *From:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu><freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>*On Behalf Of*Angela Favaro *Sent:*Sunday, June 28, 2020 1:49 PM *To:*Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> *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, seehttp://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 <BFISCHL@MGH.HARVARD.EDU <mailto:BFISCHL@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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu><freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Angela Favaro -
Douglas N. Greve -
Fischl, Bruce -
Pankush Kumar