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