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:
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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
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Any clue about what we have done wrong?
TIA.
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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