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
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.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Would it be possible to send me the dicom files?
Ruopeng
On Sep 1, 2021, at 1:14 PM, Peled, Noam <NPELED@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Noam
can you convert them with any dicom converter to any other format? dcm2nii? That kind of thing? Bruce ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Peled, Noam NPELED@mgh.harvard.edu Sent: Thursday, September 2, 2021 12:19 PM To: Freesurfer support list 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-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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes! Thanks! dmc2niix did the trick. I wonder why mri_convert failed.
Thanks! Noam
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Peled, Noam <NPELED@mgh.harvard.edumailto:NPELED@mgh.harvard.edu> Sent: Thursday, September 2, 2021 12:19 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Our dicom reader is probably too old Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Peled, Noam <NPELED@mgh.harvard.edumailto:NPELED@mgh.harvard.edu> Sent: Thursday, September 2, 2021 12:19 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Peled, Noam <NPELED@mgh.harvard.edu mailto:NPELED@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 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 <NPELED@mgh.harvard.edu <mailto: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 <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto: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 <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 <NPELED@mgh.harvard.edu <mailto:NPELED@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Great! Thanks!!
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 7, 2021 9:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Peled, Noam <NPELED@mgh.harvard.edumailto:NPELED@mgh.harvard.edu> Sent: Thursday, September 2, 2021 12:19 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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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Douglas N. Greve -
Fischl, Bruce -
Peled, Noam -
Wang, Ruopeng