There is an error before the ‘multiple frames error’:

“

Found 384 DICOM file(s)

load Image /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855821.dcm, size 114688

Warning: Unable to determine slice direction: please check whether slices are flipped

Convert 384 DICOM (224x256x192x2)

DICOM row order preserved: may appear upside down in tools that ignore spatial transforms

WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent

(0.976562,0.976562) (0.976562,0.976562) (1,0)

This is probably due to shear in the vox2ras matrix

Input Vox2RAS ------

-0.97656 0.00000 -0.00000 105.30721;

-0.00000 -0.97656 -0.00000 122.96610;

0.00000 0.00000 0.00000 -113.12712;

0.00000 0.00000 0.00000 0.00000;

TR=2000.00, TE=3.03, TI=1100.00, flip angle=15.00

i_ras = (-1, -4.897e-12, 0)

j_ras = (4.897e-12, -1, 0)

k_ras = (nan, nan, nan)

“

Let’s see if we can have it resolved first. Freesurfer internally uses dcm2niix to convert dicoms. Can you try Freesurfer dev version to see if latest dcm2niix fix the error?

Also, I noticed your SUBJECTS_DIR points to your FS install directory. It is a good idea to point it to some other directory where you have write permission.

“

INFO: SUBJECTS_DIR is /Applications/freesurfer/7.4.1/subjects

Actual FREESURFER_HOME /Applications/freesurfer/7.4.1

“

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Perumalla, Sucika
Sent: Tuesday, February 20, 2024 3:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Errors with Recon-all

Dear Freesurfer Support Services,

My name is Sucika Perumalla and I get the multiple frames errors when trying to run recon-all with my dicoms even after extracting the multiple frames. I was wondering if you can please help resolve these issues.

Thanks

_____________________________

Sucika Perumalla

Clinical Research Assistant I

Department of Neurology, Division of Movement Disorders

Brigham and Women’s Hospital

60 Fenwood Road, Boston, MA 02115

sperumalla1@bwh.harvard.edu | 508-414-2601