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