yes, in the process now of upgrading. We'll use dcm2niix internally.
On 9/7/2021 5:11 PM, Fischl, Bruce wrote:
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 visualizeFSPGR 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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