Hello,
I am evaluating FreeSurfer, installed and runned the tutorial without major troubles.
Now, we have set up the MPRAGE sequence as stated here: http://www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min.html and we have also a problem, surely a newbie and trivial one (sorry about that...).
We had a series from a test patient, but initial stage of recon-all fails (in mri-convert) with the cause "ERROR: VolSS2MosSS: number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200)"
Here is the detailed log:
-------------------------------------------------------------------------------------------
servux:~/freesurfer/subjects/ghca> recon-all -i C0001 -s test
INFO: SUBJECTS_DIR is /home/philfeu/freesurfer/subjects
Actual FREESURFER_HOME /home/philfeu/freesurfer
Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux
/home/philfeu/freesurfer/subjects/test
mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz
mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from /home/philfeu/freesurfer/subjects/ghca/C0001...
Getting Series No
INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca
INFO: Scanning for Series Number 2
Scanning Directory
INFO: found 128 files in series
INFO: loading series header info.
RunNo = 1
WARNING: Run 1 appears to be truncated
Files Found: 128, Files Expected (lRep+1): 1
FileName /home/philfeu/freesurfer/subjects/ghca/C0001
Identification
NumarisVer syngo MR A30 4VA30A
ScannerModel Symphony
PatientName TEST
Date and time
StudyDate 20080828
StudyTime 165725.921000
SeriesTime 171106.578000
AcqTime 170220.252481
Acquisition parameters
PulseSeq *tfl3d1_ns
Protocol MPRAGE VOLUM 8MIN
PhEncDir ROW
EchoNo 0
FlipAngle 7
EchoTime 3.48
InversionTime 1000
RepetitionTime 2730
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 1
SeriesNo 2
ImageNo 1
NImageRows 192
NImageCols 192
NFrames 128
SliceArraylSize 1
IsMosaic 1
ImgPos 85.7703 164.3475 80.1092
VolRes 1.2800 1.2800 1.3300
VolDim 200 200 1
Vc 0.1097 -0.9940 -0.0000
Vr -0.1091 -0.0120 -0.9940
Vs -0.9880 -0.1091 0.1097
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (200 200 1), nframes = 128, ismosaic=1
Numaris Version: syngo MR A30 4VA30A Maj = 4, Min=3, MinMin = 0
Repetition Time = 2730, TR = 2730 ms
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
FileName /home/philfeu/freesurfer/subjects/ghca/C0001
Identification
NumarisVer syngo MR A30 4VA30A
ScannerModel Symphony
PatientName TEST
Date and time
StudyDate 20080828
StudyTime 165725.921000
SeriesTime 171106.578000
AcqTime 170220.252481
Acquisition parameters
PulseSeq *tfl3d1_ns
Protocol MPRAGE VOLUM 8MIN
PhEncDir ROW
EchoNo 0
FlipAngle 7
EchoTime 3.48
InversionTime 1000
RepetitionTime 2730
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 1
SeriesNo 2
ImageNo 1
NImageRows 192
NImageCols 192
NFrames 128
SliceArraylSize 1
IsMosaic 1
ImgPos -0.0636 171.2637 83.8372
VolRes 1.2800 1.2800 1.3300
VolDim 200 200 1
Vc 0.1097 -0.9940 -0.0000
Vr -0.1091 -0.0120 -0.9940
Vs -0.9880 -0.1091 0.1097
VolCenter -0.6357 42.4228 -43.3169
TransferSyntaxUID 1.2.840.10008.1.2.1
ERROR: VolSS2MosSS: number of columns in the mosaic (192)
is not an integer multiple of the number of columns in
the image (200)
Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux
recon-all exited with ERRORS at Tue Sep 2 15:06:32 CEST 2008
-------------------------------------------------------------------------------------------
Any clue about what we have done wrong?
TIA.
-----------------------------------------------------------------------------------------------------------------------------------
Dr Philippe Feuerstein Radiologie Groupe Hospitalier du Centre Alsace Hôpital Albert Schweitzer 201, Avenue d'Alsace - BP 20129 68003 Colmar Cedex France
Tél: +33 3 89 21 25 74
mailto: philippe.feuerstein@ghca.frmailto:philippe.feuerstein@ghca.fr
Bonjour Dr Philippe
My guess is *" *
*Getting Series No *
*INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca*
*INFO: Scanning for Series Number 2*
*Scanning Directory *
*INFO: found 128 files in series*
*INFO: loading series header info.*
*"*
I think it should be better in the first runs that you convert your dicom in Alnalyze for instance using Mricro.
With the analyze file you generated from Dicom you can use mri_convert to convert it in FreeSurfer mgz and then follow the normal recon-all
I've seem sometimes my colleagues here having trouble with dealing with dicom structure when using FreeSurfer. I think this procedure helps in avoiding this problem and focusing on learning how to use FreeSurfer. If you need any additional help contact me through the FreeSurfer Mailing.
Best Regards,
PPJ
2008/9/3 Feuerstein Philippe Philippe.Feuerstein@ghca.fr
Hello,
I am evaluating FreeSurfer, installed and runned the tutorial without major troubles.
Now, we have set up the MPRAGE sequence as stated here: http://www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min.htmlhttp://www.nmr.mgh.harvard.edu/%7Eandre/Sequences/SagMPR8Min.html and we have also a problem, surely a newbie and trivial one (sorry about that...).
We had a series from a test patient, but initial stage of recon-all fails (in mri-convert) with the cause "ERROR: VolSS2MosSS: number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200)"
Here is the detailed log:
servux:~/freesurfer/subjects/ghca> recon-all -i C0001 -s test
INFO: SUBJECTS_DIR is /home/philfeu/freesurfer/subjects
Actual FREESURFER_HOME /home/philfeu/freesurfer
Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux
/home/philfeu/freesurfer/subjects/test
mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz
mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from /home/philfeu/freesurfer/subjects/ghca/C0001...
Getting Series No
INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca
INFO: Scanning for Series Number 2
Scanning Directory
INFO: found 128 files in series
INFO: loading series header info.
RunNo = 1
WARNING: Run 1 appears to be truncated
Files Found: 128, Files Expected (lRep+1): 1
FileName /home/philfeu/freesurfer/subjects/ghca/C0001
Identification
NumarisVer syngo MR A30 4VA30A ScannerModel Symphony PatientName TESTDate and time
StudyDate 20080828 StudyTime 165725.921000 SeriesTime 171106.578000 AcqTime 170220.252481Acquisition parameters
PulseSeq *tfl3d1_ns Protocol MPRAGE VOLUM 8MIN PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.48 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256Image information
RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 192 NImageCols 192 NFrames 128 SliceArraylSize 1 IsMosaic 1 ImgPos 85.7703 164.3475 80.1092 VolRes 1.2800 1.2800 1.3300 VolDim 200 200 1 Vc 0.1097 -0.9940 -0.0000 Vr -0.1091 -0.0120 -0.9940 Vs -0.9880 -0.1091 0.1097 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1INFO: sorting.
INFO: (200 200 1), nframes = 128, ismosaic=1
Numaris Version: syngo MR A30 4VA30A Maj = 4, Min=3, MinMin = 0
Repetition Time = 2730, TR = 2730 ms
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
FileName /home/philfeu/freesurfer/subjects/ghca/C0001
Identification
NumarisVer syngo MR A30 4VA30A ScannerModel Symphony PatientName TESTDate and time
StudyDate 20080828 StudyTime 165725.921000 SeriesTime 171106.578000 AcqTime 170220.252481Acquisition parameters
PulseSeq *tfl3d1_ns Protocol MPRAGE VOLUM 8MIN PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.48 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256Image information
RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 192 NImageCols 192 NFrames 128 SliceArraylSize 1 IsMosaic 1 ImgPos -0.0636 171.2637 83.8372 VolRes 1.2800 1.2800 1.3300 VolDim 200 200 1 Vc 0.1097 -0.9940 -0.0000 Vr -0.1091 -0.0120 -0.9940 Vs -0.9880 -0.1091 0.1097 VolCenter -0.6357 42.4228 -43.3169 TransferSyntaxUID 1.2.840.10008.1.2.1ERROR: VolSS2MosSS: number of columns in the mosaic (192)
is not an integer multiple of the number of columns in
the image (200)
Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux
recon-all exited with ERRORS at Tue Sep 2 15:06:32 CEST 2008
Any clue about what we have done wrong?
TIA.
Dr Philippe Feuerstein Radiologie Groupe Hospitalier du Centre Alsace Hôpital Albert Schweitzer 201, Avenue d'Alsace - BP 20129 68003 Colmar Cedex France
Tél: +33 3 89 21 25 74
mailto: philippe.feuerstein@ghca.fr
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for your advice.
Unfortunately, I first tried recon-all but failed with the same cause (number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200); it is just to have a more detailed output that I used mri-convert (that I guessed to be the first step in recon-all).
All the best.
________________________________ From: Pedro Paulo de Magalhães Oliveira Junior [mailto:ppj@netfilter.com.br] Sent: Wednesday, September 03, 2008 2:56 PM To: Feuerstein Philippe Cc: freesurfer@nmr.mgh.harvard.edu Subject: *** Detected as Spam *** Re: [Freesurfer] Newbie problem...
Bonjour Dr Philippe
My guess is "
Getting Series No
INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca
INFO: Scanning for Series Number 2
Scanning Directory
INFO: found 128 files in series
INFO: loading series header info.
"
I think it should be better in the first runs that you convert your dicom in Alnalyze for instance using Mricro.
With the analyze file you generated from Dicom you can use mri_convert to convert it in FreeSurfer mgz and then follow the normal recon-all
I've seem sometimes my colleagues here having trouble with dealing with dicom structure when using FreeSurfer. I think this procedure helps in avoiding this problem and focusing on learning how to use FreeSurfer.
If you need any additional help contact me through the FreeSurfer Mailing.
Best Regards,
PPJ
2008/9/3 Feuerstein Philippe <Philippe.Feuerstein@ghca.frmailto:Philippe.Feuerstein@ghca.fr> Hello,
I am evaluating FreeSurfer, installed and runned the tutorial without major troubles.
Now, we have set up the MPRAGE sequence as stated here: http://www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min.html and we have also a problem, surely a newbie and trivial one (sorry about that...).
We had a series from a test patient, but initial stage of recon-all fails (in mri-convert) with the cause "ERROR: VolSS2MosSS: number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200)"
Here is the detailed log:
-------------------------------------------------------------------------------------------
servux:~/freesurfer/subjects/ghca> recon-all -i C0001 -s test
INFO: SUBJECTS_DIR is /home/philfeu/freesurfer/subjects
Actual FREESURFER_HOME /home/philfeu/freesurfer
Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux
/home/philfeu/freesurfer/subjects/test
mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz
mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.146.2.2http://1.146.2.2 2008/03/02 02:53:20 nicks Exp $
reading from /home/philfeu/freesurfer/subjects/ghca/C0001...
Getting Series No
INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca
INFO: Scanning for Series Number 2
Scanning Directory
INFO: found 128 files in series
INFO: loading series header info.
RunNo = 1
WARNING: Run 1 appears to be truncated
Files Found: 128, Files Expected (lRep+1): 1
FileName /home/philfeu/freesurfer/subjects/ghca/C0001
Identification
NumarisVer syngo MR A30 4VA30A
ScannerModel Symphony
PatientName TEST
Date and time
StudyDate 20080828
StudyTime 165725.921000
SeriesTime 171106.578000
AcqTime 170220.252481
Acquisition parameters
PulseSeq *tfl3d1_ns
Protocol MPRAGE VOLUM 8MIN
PhEncDir ROW
EchoNo 0
FlipAngle 7
EchoTime 3.48
InversionTime 1000
RepetitionTime 2730
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 1
SeriesNo 2
ImageNo 1
NImageRows 192
NImageCols 192
NFrames 128
SliceArraylSize 1
IsMosaic 1
ImgPos 85.7703 164.3475 80.1092
VolRes 1.2800 1.2800 1.3300
VolDim 200 200 1
Vc 0.1097 -0.9940 -0.0000
Vr -0.1091 -0.0120 -0.9940
Vs -0.9880 -0.1091 0.1097
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (200 200 1), nframes = 128, ismosaic=1
Numaris Version: syngo MR A30 4VA30A Maj = 4, Min=3, MinMin = 0
Repetition Time = 2730, TR = 2730 ms
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
FileName /home/philfeu/freesurfer/subjects/ghca/C0001
Identification
NumarisVer syngo MR A30 4VA30A
ScannerModel Symphony
PatientName TEST
Date and time
StudyDate 20080828
StudyTime 165725.921000
SeriesTime 171106.578000
AcqTime 170220.252481
Acquisition parameters
PulseSeq *tfl3d1_ns
Protocol MPRAGE VOLUM 8MIN
PhEncDir ROW
EchoNo 0
FlipAngle 7
EchoTime 3.48
InversionTime 1000
RepetitionTime 2730
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 1
SeriesNo 2
ImageNo 1
NImageRows 192
NImageCols 192
NFrames 128
SliceArraylSize 1
IsMosaic 1
ImgPos -0.0636 171.2637 83.8372
VolRes 1.2800 1.2800 1.3300
VolDim 200 200 1
Vc 0.1097 -0.9940 -0.0000
Vr -0.1091 -0.0120 -0.9940
Vs -0.9880 -0.1091 0.1097
VolCenter -0.6357 42.4228 -43.3169
TransferSyntaxUID 1.2.840.10008.1.2.1
ERROR: VolSS2MosSS: number of columns in the mosaic (192)
is not an integer multiple of the number of columns in
the image (200)
Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux
recon-all exited with ERRORS at Tue Sep 2 15:06:32 CEST 2008
-------------------------------------------------------------------------------------------
Any clue about what we have done wrong?
TIA.
-----------------------------------------------------------------------------------------------------------------------------------
Dr Philippe Feuerstein Radiologie Groupe Hospitalier du Centre Alsace Hôpital Albert Schweitzer 201, Avenue d'Alsace - BP 20129 68003 Colmar Cedex France
Tél: +33 3 89 21 25 74
mailto: philippe.feuerstein@ghca.frmailto:philippe.feuerstein@ghca.fr
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom
Feuerstein,
One thing I noticed in the output is that there are 128 frames (NFrames = 128), which is unusual. Typically there is just one frame in a structural run.
Try running this command in the directory where your (Siemens) dicoms are located:
unpacksdcmdir -src . -targ . -scanonly scan.dat
this will parse the files and produces a file called unpack.log. look for the series that appears to be the structural, then type:
mri_convert <firststructuraldicom> 001.mgz
if that works (ie, tkmedit -f 001.mgz looks good), then use that dicom in the -i arg of recon-all.
Nick
On Thu, 2008-09-04 at 11:30 +0200, Feuerstein Philippe wrote:
Thanks for your advice.
Unfortunately, I first tried recon-all but failed with the same cause (number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200); it is just to have a more detailed output that I used mri-convert (that I guessed to be the first step in recon-all).
All the best.
From: Pedro Paulo de Magalhães Oliveira Junior [mailto:ppj@netfilter.com.br] Sent: Wednesday, September 03, 2008 2:56 PM To: Feuerstein Philippe Cc: freesurfer@nmr.mgh.harvard.edu Subject: *** Detected as Spam *** Re: [Freesurfer] Newbie problem...
Bonjour Dr Philippe
My guess is "
Getting Series No
INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca
INFO: Scanning for Series Number 2
Scanning Directory
INFO: found 128 files in series
INFO: loading series header info.
"
I think it should be better in the first runs that you convert your dicom in Alnalyze for instance using Mricro.
With the analyze file you generated from Dicom you can use mri_convert to convert it in FreeSurfer mgz and then follow the normal recon-all
I've seem sometimes my colleagues here having trouble with dealing with dicom structure when using FreeSurfer. I think this procedure helps in avoiding this problem and focusing on learning how to use FreeSurfer.
If you need any additional help contact me through the FreeSurfer Mailing.
Best Regards,
PPJ
2008/9/3 Feuerstein Philippe Philippe.Feuerstein@ghca.fr Hello,
I am evaluating FreeSurfer, installed and runned the tutorial without major troubles. Now, we have set up the MPRAGE sequence as stated here: http://www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min.html and we have also a problem, surely a newbie and trivial one (sorry about that...). We had a series from a test patient, but initial stage of recon-all fails (in mri-convert) with the cause "ERROR: VolSS2MosSS: number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200)" Here is the detailed log: ------------------------------------------------------------------------------------------- servux:~/freesurfer/subjects/ghca> recon-all -i C0001 -s test INFO: SUBJECTS_DIR is /home/philfeu/freesurfer/subjects Actual FREESURFER_HOME /home/philfeu/freesurfer Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux /home/philfeu/freesurfer/subjects/test mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz $Id: mri_convert.c,v MailScanner has detected a possible fraud attempt from "1.146.2.2" claiming to beMailScanner warning: numerical links are often malicious: 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /home/philfeu/freesurfer/subjects/ghca/C0001... Getting Series No INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca INFO: Scanning for Series Number 2 Scanning Directory INFO: found 128 files in series INFO: loading series header info. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 128, Files Expected (lRep+1): 1 FileName /home/philfeu/freesurfer/subjects/ghca/C0001 Identification NumarisVer syngo MR A30 4VA30A ScannerModel Symphony PatientName TEST Date and time StudyDate 20080828 StudyTime 165725.921000 SeriesTime 171106.578000 AcqTime 170220.252481 Acquisition parameters PulseSeq *tfl3d1_ns Protocol MPRAGE VOLUM 8MIN PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.48 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 192 NImageCols 192 NFrames 128 SliceArraylSize 1 IsMosaic 1 ImgPos 85.7703 164.3475 80.1092 VolRes 1.2800 1.2800 1.3300 VolDim 200 200 1 Vc 0.1097 -0.9940 -0.0000 Vr -0.1091 -0.0120 -0.9940 Vs -0.9880 -0.1091 0.1097 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (200 200 1), nframes = 128, ismosaic=1 Numaris Version: syngo MR A30 4VA30A Maj = 4, Min=3, MinMin = 0 Repetition Time = 2730, TR = 2730 ms AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /home/philfeu/freesurfer/subjects/ghca/C0001 Identification NumarisVer syngo MR A30 4VA30A ScannerModel Symphony PatientName TEST Date and time StudyDate 20080828 StudyTime 165725.921000 SeriesTime 171106.578000 AcqTime 170220.252481 Acquisition parameters PulseSeq *tfl3d1_ns Protocol MPRAGE VOLUM 8MIN PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.48 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 192 NImageCols 192 NFrames 128 SliceArraylSize 1 IsMosaic 1 ImgPos -0.0636 171.2637 83.8372 VolRes 1.2800 1.2800 1.3300 VolDim 200 200 1 Vc 0.1097 -0.9940 -0.0000 Vr -0.1091 -0.0120 -0.9940 Vs -0.9880 -0.1091 0.1097 VolCenter -0.6357 42.4228 -43.3169 TransferSyntaxUID 1.2.840.10008.1.2.1 ERROR: VolSS2MosSS: number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200) Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Sep 2 15:06:32 CEST 2008 ------------------------------------------------------------------------------------------- Any clue about what we have done wrong? TIA. ----------------------------------------------------------------------------------------------------------------------------------- Dr Philippe Feuerstein Radiologie Groupe Hospitalier du Centre Alsace Hôpital Albert Schweitzer 201, Avenue d'Alsace - BP 20129 68003 Colmar Cedex France Tél: +33 3 89 21 25 74 mailto: philippe.feuerstein@ghca.fr _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try running mri_convert with the -in_type dicom. It is trying to read it as a siemens dicom, but there appears to be something it does not expect in the header. The generic will probably work.
doug
Feuerstein Philippe wrote:
Thanks for your advice.
Unfortunately, I first tried recon-all but failed with the same cause (number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200); it is just to have a more detailed output that I used mri-convert (that I guessed to be the first step in recon-all).
All the best.
From: Pedro Paulo de Magalhães Oliveira Junior [mailto:ppj@netfilter.com.br] Sent: Wednesday, September 03, 2008 2:56 PM To: Feuerstein Philippe Cc: freesurfer@nmr.mgh.harvard.edu Subject: *** Detected as Spam *** Re: [Freesurfer] Newbie problem...
Bonjour Dr Philippe
My guess is "
Getting Series No
INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca
INFO: Scanning for Series Number 2
Scanning Directory
INFO: found 128 files in series
INFO: loading series header info.
"
I think it should be better in the first runs that you convert your dicom in Alnalyze for instance using Mricro.
With the analyze file you generated from Dicom you can use mri_convert to convert it in FreeSurfer mgz and then follow the normal recon-all
I've seem sometimes my colleagues here having trouble with dealing with dicom structure when using FreeSurfer. I think this procedure helps in avoiding this problem and focusing on learning how to use FreeSurfer.
If you need any additional help contact me through the FreeSurfer Mailing.
Best Regards,
PPJ
2008/9/3 Feuerstein Philippe <Philippe.Feuerstein@ghca.fr mailto:Philippe.Feuerstein@ghca.fr>
Hello, I am evaluating FreeSurfer, installed and runned the tutorial without major troubles. Now, we have set up the MPRAGE sequence as stated here: http://www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min.html and we have also a problem, surely a newbie and trivial one (sorry about that...). We had a series from a test patient, but initial stage of recon-all fails (in mri-convert) with the cause "ERROR: VolSS2MosSS: number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200)" Here is the detailed log: ------------------------------------------------------------------------------------------- servux:~/freesurfer/subjects/ghca> recon-all -i C0001 -s test INFO: SUBJECTS_DIR is /home/philfeu/freesurfer/subjects Actual FREESURFER_HOME /home/philfeu/freesurfer Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux /home/philfeu/freesurfer/subjects/test mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz $Id: mri_convert.c,v MailScanner has detected a possible fraud attempt from "1.146.2.2" claiming to be MailScanner warning: numerical links are often malicious: 1.146.2.2 <http://1.146.2.2> 2008/03/02 02:53:20 nicks Exp $ reading from /home/philfeu/freesurfer/subjects/ghca/C0001... Getting Series No INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca INFO: Scanning for Series Number 2 Scanning Directory INFO: found 128 files in series INFO: loading series header info. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 128, Files Expected (lRep+1): 1 FileName /home/philfeu/freesurfer/subjects/ghca/C0001 Identification NumarisVer syngo MR A30 4VA30A ScannerModel Symphony PatientName TEST Date and time StudyDate 20080828 StudyTime 165725.921000 SeriesTime 171106.578000 AcqTime 170220.252481 Acquisition parameters PulseSeq *tfl3d1_ns Protocol MPRAGE VOLUM 8MIN PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.48 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 192 NImageCols 192 NFrames 128 SliceArraylSize 1 IsMosaic 1 ImgPos 85.7703 164.3475 80.1092 VolRes 1.2800 1.2800 1.3300 VolDim 200 200 1 Vc 0.1097 -0.9940 -0.0000 Vr -0.1091 -0.0120 -0.9940 Vs -0.9880 -0.1091 0.1097 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (200 200 1), nframes = 128, ismosaic=1 Numaris Version: syngo MR A30 4VA30A Maj = 4, Min=3, MinMin = 0 Repetition Time = 2730, TR = 2730 ms AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /home/philfeu/freesurfer/subjects/ghca/C0001 Identification NumarisVer syngo MR A30 4VA30A ScannerModel Symphony PatientName TEST Date and time StudyDate 20080828 StudyTime 165725.921000 SeriesTime 171106.578000 AcqTime 170220.252481 Acquisition parameters PulseSeq *tfl3d1_ns Protocol MPRAGE VOLUM 8MIN PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.48 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 192 NImageCols 192 NFrames 128 SliceArraylSize 1 IsMosaic 1 ImgPos -0.0636 171.2637 83.8372 VolRes 1.2800 1.2800 1.3300 VolDim 200 200 1 Vc 0.1097 -0.9940 -0.0000 Vr -0.1091 -0.0120 -0.9940 Vs -0.9880 -0.1091 0.1097 VolCenter -0.6357 42.4228 -43.3169 TransferSyntaxUID 1.2.840.10008.1.2.1 ERROR: VolSS2MosSS: number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200) Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Sep 2 15:06:32 CEST 2008 ------------------------------------------------------------------------------------------- Any clue about what we have done wrong? TIA. ----------------------------------------------------------------------------------------------------------------------------------- Dr Philippe Feuerstein Radiologie Groupe Hospitalier du Centre Alsace Hôpital Albert Schweitzer 201, Avenue d'Alsace - BP 20129 68003 Colmar Cedex France Tél: +33 3 89 21 25 74 mailto: philippe.feuerstein@ghca.fr <mailto:philippe.feuerstein@ghca.fr> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom
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Doug Greve -
Feuerstein Philippe -
Nick Schmansky -
Pedro Paulo de Magalhães Oliveira Junior