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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
<bfis...@mgh.harvard.edu <mailto:bfis...@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-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 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
<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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