Are you sure 102.mgz is from our analysis previously? We typically name the
volumes 001.mgz, 002.mgz, etc....
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
<bfis...@mgh.harvard.edu<mailto: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
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