Hello Antti,
It may be possible that you’ve run out of space and the full volumes were not written. You can check by using: df -h /path/to/file Similarly, you can run mri_info on the input files to see how many frames there are and where the discrepancy between the volumes set to x and y are arising.
Best, Matt
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Date: Saturday, January 9, 2021 at 9:06 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] dt_recon error: dimension mismatch between y and X
External Email - Use Caution Dear FS experts,
I’m attempting to run dt_recon on my own DWI DICOM file with registration to corresponding structural data, as described in FS diffusion tutorial (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0https://secure-web.cisco.com/1zJ4MwZjBaZucnMqD07gGW81VRhJOuT2j8dl2ILpEXoVY03-Gt9rt0ZuiEYcP2yVe5O2g1zNh0QohzvsjRUbksy7buOnBgwp6xGeDgIi8lITcB6n4WK1aY_txDjItVwJEpBvgeZojTWziZ8-NLiamr-dV3lFnWVCvRmJq16D-Av42R15tqFdYYxzgMfGvGKQTSXh1N4-liUveNX58tqS9xPj6xI7XIWvWPctTpzEMxgPfKFkBGGPfBeoyZqMVEnlmsSTDkgt0uG9jl13kDKmOIA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FDiffusionV6.0) I’m using FS version freesurfer-darwin-macOS-7.1.1-20200811-8b40551 on Mac (MacOS Big Sur v. 11.1). I’ve already succesfully run recon-all on the T1 scan. However, when I’m running the dt_recon, I’m getting the following error:
Command I’m using: dt_recon --i $TUTORIAL_DIR/$subj/orig/DTI/S142783/NIFD_1_S_0001_MR_dti_WIP_b2000_64dir__br_raw_20120306104435815_50_S142783_I288323.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon
ERROR: dimension mismatch between y and X. y has 65 inputs, X has 66 rows.
I’ve searched the archive, however not finding any similar issues. Does anyone have an idea how to solve this error? Attached is the dt_recon.log.
Best, Antti Cajanus