Glad to hear it Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of William McCuddy AZ-Phoenix Sent: Saturday, December 11, 2021 3:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer recon-all error “mri_convert: extra argument”

External Email - Use Caution wow, that did the trick! recon-all is off and running. Thank you for catching this!

Travis

On Sat, Dec 11, 2021 at 1:24 PM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: USE CAUTION - EXTERNAL EMAIL ________________________________ Hi Travis

It is because you have a space “ “ in your path:

Processed Data

If you rename the path to

Processed_Data

It should work fine Bruce From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of William McCuddy AZ-Phoenix Sent: Saturday, December 11, 2021 3:13 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer recon-all error “mri_convert: extra argument”

External Email - Use Caution

Hello Freesurfer Community,

I'm new to freesurfer and could use some help with recon-all on a single subject. The input file is a 3D T1 WAND from a Philips scanner. I used dcm2niix to convert from dicom to nifti. I can open the nifti file and everything looks normal. nNfti header info displayed in screenshot below and computer specs are listed in the attached recon-all log file (shortened). Not sure what the “mri_convert: extra argument” problem is. If anyone knows what I’m doing wrong, I would love some assistance!

Thanks,

Travis

Original T1 (after conversion from dicom) [cid:image001.png@01D7EEAD.8FB86BE0]

Fri Dec 10 20:43:44 MST 2021 cd /usr/local/freesurfer/7.2.0/subjects/KH setenv SUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjects /usr/local/freesurfer/7.2.0/bin/recon-all -s KH -i KH_T1.nii.gz -all -parallel -openmp 6 subjid KH setenv SUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjects FREESURFER_HOME /usr/local/freesurfer/7.2.0 Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0 build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Linux BarrowPrismProcess 5.11.0-41-generic #45~20.04.1-Ubuntu SMP Wed Nov 10 10:20:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux total used free shared buff/cache available Mem: 31Gi 4.8Gi 4.1Gi 24Mi 22Gi 25Gi Swap: 2.0Gi 2.0Mi 2.0Gi ######################################## program versions used 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) 7.2.0 ####################################### GCADIR /usr/local/freesurfer/7.2.0/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/7.2.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /usr/local/freesurfer/7.2.0/subjects/KH mri_convert /home/prism/Desktop/Processed Data/KH_T1.nii.gz /usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz mri_convert /home/prism/Desktop/Processed Data/KH_T1.nii.gz /usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz mri_convert: extra argument ("/usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz") type mri_convert -u for usage Command exited with non-zero status 1 @#@FSTIME 2021:12:10:20:43:45 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 100% M 6284 F 0 R 247 W 0 c 0 w 1 I 0 O 0 L 0.32 0.25 0.21 @#@FSLOADPOST 2021:12:10:20:43:45 mri_convert N 3 0.32 0.25 0.21 Linux BarrowPrismProcess 5.11.0-41-generic #45~20.04.1-Ubuntu SMP Wed Nov 10 10:20:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s KH exited with ERRORS at Fri Dec 10 20:43:45 MST 2021 To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttps://secure-web.cisco.com/13sjWFha0n8fNWCE_a8WYSqy6Q3zdJxwlnV0NWfQFJE-nkxDlxet83b_hv0ATmn6VZeIzeVM6nUyVqX01VAC__lAlAdoH3QZJO3rv7NiQ8hgA64E0r1K0yU9tb4HYHFqyw0CMrJpJL-OiRqr_tUZDnYihEnGGh8lbUVUwwSuDQhj2qw_gW0DYGuXCw416YXkuiPpI0bELc12z2Tbm4nfFdL4f85R6hxQXXlHlWszSCXsrGih5a4TibdXqFlkNab9dwW4MNG6Xn8qw4xcAMJwi_fcmvM1yd9bQn7R6_id-xWDnfYsoTWqJ8Y9J7aN-37Yjpt0te2g8XlD2lDVxYtDsGw/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fsecure-web.cisco.com%2F13ddiImmrJeyHcBtuL-2JQaEFuG60p6qT6OFYGZt3WA_uSvqI7pQar9v4E1Y3tAI7z9vXTThqivei1ezuBmvlgvnGKYjRZ-KkOvLJ6ku27j6LyonW035JoSWocyBFf2Bzk0k1TbxKHSkpUZaBHe_lNEBBmm2rJCqiuzOPqUT6x_n8ab-Wu9kYttwviNEXxeCOh6FjKGlHcehaVE0zOhjpqFWqGGidfFIXkNCg7JTaDe-55xGYEKc3KnvBFSG7RMz2EYXGTdBhbp8hqSfVKMqpXYbm00es2MSnEbHv1LQ8AC1juSG_-cyNi7fv5qX-Mv6P%2Fhttp%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FBugReporting__%3BJSUlJSU%21%21CqLityr3mSQ%21UMRDlRtS79_xpOjVg04BHVSMwFn4tdKfl1K1oytYdgkAthl9YWBsXwlNB9zDYs7gN3REfpGb5A%24

-- William T. McCuddy, PhD Clinical Neuropsychologist Department of Clinical Neuropsychology Joint Appointment in Neuroradiology

Barrow Neurological Institute Dignity Health I St. Joseph’s Hospital and Medical Center 222 W. Thomas Rd, Suite 315 Phoenix, AZ 85013 602.406.3671 (O) 602.406.6115 (F)

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