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
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-- ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom