Can you send the log file of the run using the nifti as input? The file you attached is for dicom input.
On 4/8/2021 8:39 AM, Banu Femir wrote:
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Dear FreeSurfer Developers,
I've a problem that cannot solve for the last week. I am using virtual box, FS7 on my windows. I run reconall for Bert and checked that it is working.I have an MRI scan of sepstic patients that I got via CD, these are DICOM files but does not end with .dcm.
When I try to run reconall, for dcm images I got the following error (the longer version is in the attachment)
........ Loading pixel data JPEG compressed, decompressing cd /home/developer/Documents/7.1.0-1/subjects/sepsis2 fsdcmdecompress --i /home/developer/Documents/7.1.0-1/subjects/D_000001/F_000001 --o /tmp/developer.tmp.decompressed.dcm.0oOV4x --jpeg >& /tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out ERROR: 512, see /tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out for more details Command exited with non-zero status 1 @#@FSTIME 2021:04:08:08:29:16 mri_convert N 2 e 1.97 S 1.19 U 0.60 P 91% M 9200 F 2 R 999 W 0 c 174 w 356 I 32240 O 0 L 0.55 0.33 0.41 @#@FSLOADPOST 2021:04:08:08:29:18 mri_convert N 2 0.55 0.33 0.41 Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sepsis2 exited with ERRORS at Thu Apr 8 08:29:18 EDT 202
I converted files to nii, this time I decided to run reconall on nii images, it took more time but again failed on talairach transform.
I tried to run on different shells but ended up with the same problem. Is it related with my MRI data or computer, how can I understand that?
Many thanks! Banu
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