Hello everyone,

I am having trouble getting past the very first stages of trac-all -prep.

I am using FreeSurfer 7.3.2. I tried several workarounds based on previous answers to similar problems in this mailing list, but I am unsuccessful each time.

First, when I try to run trac-all -prep without any configuration file, using only the defaults, it prints out an error:

trac-all -prep -s sub-01 -i $SUBJECTS_DIR/raw/sub-01/dwi/1_0000.dcm
ERROR: for B0 distortion correction with reverse-polarity DWIs
ERROR: or for model-based eddy-current distortion correction,
ERROR: must specify PE direction

As I understand it, the default version of trac-all should assume default deb0=0, and not look for reverse-polarity images to do distortion correction for TOPUP.

Then, I tried to perform the analysis using the configuration file and specify that I do not want to perform correction based on reverse-polarity images or phase maps (my data don't have these), by explicitly entering "set dob0 = 0". The problem persisted. I did what a previous user was told to do - set "pedir" and "epifactor" and "echospacing" manually.

Then, I ran into the final error which I cannot overcome.

No matter what I do, it ends in an error:

mv: cannot stat '/home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz': No such file or directory

It seems it cannot create this file.

Earlier in the log there is also a previously mentioned error:

It appears to be a problem with converting into LAS.

(Previously there was mention of there being a wrong "trac-preproc" file for runs with only 1 subject, but my problem remains when trying to run single and multiple subjects. I also tried to change my trac-preproc file to the versions from previous answers, with no luck).

When I check the dmri folder the dwi_orig.1.bvals and dwi_orig.1.bvecs, and dwi_orig_las.1.bvals files contain correct values, but dwi_orig_las.1.bvecs contains only zeros.

When I run mri_info on dwi_orig.1.nii.gz I get this:

Volume information for sub-01/dmri/dwi_orig.1.nii.gz
          type: nii
    dimensions: 128 x 128 x 60 x 76
   voxel sizes: 1.718750, 1.718750, 2.200000
          type: SHORT (4)
           fov: 220.000
           dof: 1
        xstart: -110.0, xend: 110.0
        ystart: -110.0, yend: 110.0
        zstart: -66.0, zend: 66.0
            TR: 7100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 76
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r =  -0.9959, y_r =  -0.0243, z_r =  -0.0868, c_r =    -0.4050
              : x_a =   0.0326, y_a =  -0.9949, z_a =  -0.0955, c_a =   -21.6846
              : x_s =  -0.0841, y_s =  -0.0979, z_s =   0.9916, c_s =     7.5075
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
               -1.7117  -0.0418  -0.1910   117.5550
                0.0561  -1.7100  -0.2100    90.4641
               -0.1445  -0.1683   2.1816   -37.9249
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant 6.49902

ras to voxel transform:
               -0.5794   0.0190  -0.0489    64.5443
               -0.0142  -0.5789  -0.0570    51.8698
               -0.0395  -0.0434   0.4507    25.6592
                0.0000   0.0000   0.0000     1.0000

"PhEncDir" shows UNKNOWN, but as I said, my config file contains "set pedir = (AP)".

I also tried to do the analysis on FreeSurfer 7.2 and the develeopment version, but no luck.

I would appreciate any input into how to solve this problem.

Regards,

SJ.