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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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>
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 <NPELED@mgh.harvard.edu> wrote:
The same error.
Also, when trying to run recon-all on these files.
Thanks,
Noam
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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>
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 <NPELED@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
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