Our dicom reader is probably too old Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Peled, Noam Sent: Tuesday, September 7, 2021 2:56 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number
Yes! Thanks! dmc2niix did the trick. I wonder why mri_convert failed. Thanks! Noam From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Fischl, Bruce Sent: Thursday, September 2, 2021 12:44 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number Hi Noam can you convert them with any dicom converter to any other format? dcm2nii? That kind of thing? Bruce ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Peled, Noam <npe...@mgh.harvard.edu<mailto:npe...@mgh.harvard.edu>> Sent: Thursday, September 2, 2021 12:19 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number Unfortunately, it's patient data from another hospital, and I also can't access the files. I'm just helping them to use FreeSurfer. Is there a debug version that outputs more information? The temp file (basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg) is empty. Thanks! Noam From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Wang, Ruopeng Sent: Thursday, September 2, 2021 10:00 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number Would it be possible to send me the dicom files? Ruopeng On Sep 1, 2021, at 1:14 PM, Peled, Noam <npe...@mgh.harvard.edu<mailto:npe...@mgh.harvard.edu>> wrote: The same error. Also, when trying to run recon-all on these files. Thanks, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Wang, Ruopeng Sent: Wednesday, September 1, 2021 12:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number What if you use mri_convert to convert them to a mgz or nii volume? Do you get the same error? Ruopeng On Sep 1, 2021, at 10:52 AM, Peled, Noam <npe...@mgh.harvard.edu<mailto:npe...@mgh.harvard.edu>> wrote: Hello! I'm trying to use freeview to visualize FSPGR dicoms files. I'm using ubuntu 18.04 with tcsh shell. I'm getting the following error: sh: 1: Syntax error: Bad fd number Here is the full error message: Starting DICOMRead2() dcmfile =~/Desktop/04254335/05641194 dcmdir = ~/Desktop/04254335 Ref Series No = 3 Found 200 files, checking for dicoms Found 200 files, checking for dicoms 5 /05641194 Found 198 dicom files in series. Found 198 dicom files in series. oms 5 /05641194 First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 198 ndcmfiles = 198 INFO: rescale not needed PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd ~/Desktop fsdcmdecompress --i ~/Desktop/04254335/05641194 --o /tmp/basuia.tmp.decompressed.dcm.yK9HZZ --jpeg >& /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out sh: 1: Syntax error: Bad fd number ERROR: 512, see /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out for more details QObject::~QObject: Timers cannot be stopped from another thread Thanks, Noam _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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