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