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.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 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 <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

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_______________________________________________
Freesurfer mailing list
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