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 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
 

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Netfilter & SpeedComm Telecom