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”
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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.edu> wrote:
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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.edu <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.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)
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
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--
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)
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