One more comment

if you are looking to run recon-all after that, that 001.mgz should be inside orig/

cd $SUBJECTS_DIR/mri/orig mri_convert 001088.dcm 001.mgz

should work I guess.

Even that step is not needed in the case of recon-all, see

http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer

Specifically the "Getting Started With your Own Data" section

Krish

On Apr 16, 2009, at 1:49 PM, Bruce Fischl wrote:

just give it a single dicom file in the right series, not all of them.

cheers, Bruce On Thu, 16 Apr 2009, Gabriel Go.Es. wrote:

...

Dear colleages,

I am trying to convert my dicom files to .mgz from Freesurfer (release 4.2) by using the mri_convert command, but it provides me the following error:

[root@localhost ~]$ cd /root/trabajo/freesurfer/subjects/mci_001/mri [root@localhost mri]$ mri_convert -it dicom -ot mgz orig/001*.dcm 001.mgz mri_convert -it dicom -ot mgz orig/001088.dcm orig/001089.dcm orig/ 001090.dcm orig/001091.dcm orig/001092.dcm orig/001093.dcm orig/ 001094.dcm orig/001095.dcm orig/001096.dcm orig/001097.dcm orig/ 001098.dcm orig/001099.dcm orig/001100.dcm orig/001101.dcm orig/ 001102.dcm orig/001103.dcm orig/001104.dcm orig/001105.dcm orig/ 001106.dcm orig/001107.dcm orig/001108.dcm orig/001109.dcm orig/ 001110.dcm orig/001111.dcm orig/001112.dcm orig/001113.dcm orig/ 001114.dcm orig/001115.dcm orig/001116.dcm orig/001117.dcm orig/ 001118.dcm orig/001119.dcm orig/001120.dcm orig/001121.dcm orig/ 001122.dcm orig/001123.dcm orig/001124.dcm orig/001125.dcm orig/ 001126.dcm orig/001127.dcm orig/001128.dcm orig/001129.dcm orig/ 001130.dcm orig/001131.dcm orig/001132.dcm orig/001133.dcm orig/ 001134.dcm orig/001135.dcm orig/001136.dcm orig/001137.dcm orig/ 001138.dcm orig/001139.dcm orig/001140.dcm orig/001141.dcm orig/ 001142.dcm orig/001143.dcm orig/001144.dcm orig/001145.dcm orig/ 001146.dcm orig/001147.dcm orig/001148.dcm orig/001149.dcm orig/ 001150.dcm orig/001151.dcm orig/001152.dcm orig/001153.dcm orig/ 001154.dcm orig/001155.dcm orig/001156.dcm orig/001157.dcm orig/ 001158.dcm orig/001159.dcm orig/001160.dcm orig/001161.dcm orig/ 001162.dcm orig/001163.dcm orig/001164.dcm orig/001165.dcm orig/ 001166.dcm orig/001167.dcm orig/001168.dcm orig/001169.dcm orig/ 001170.dcm orig/001171.dcm orig/001172.dcm orig/001173.dcm orig/ 001174.dcm orig/001175.dcm orig/001176.dcm orig/001177.dcm orig/ 001178.dcm orig/001179.dcm orig/001180.dcm orig/001181.dcm orig/ 001182.dcm orig/001183.dcm orig/001184.dcm orig/001185.dcm orig/ 001186.dcm orig/001187.dcm orig/001188.dcm orig/001189.dcm orig/ 001190.dcm orig/001191.dcm orig/001192.dcm orig/001193.dcm orig/ 001194.dcm orig/001195.dcm orig/001196.dcm orig/001197.dcm orig/ 001198.dcm orig/001199.dcm orig/001200.dcm orig/001201.dcm orig/ 001202.dcm orig/001203.dcm orig/001204.dcm orig/001205.dcm orig/ 001206.dcm orig/001207.dcm orig/001208.dcm orig/001209.dcm orig/ 001210.dcm orig/001211.dcm orig/001212.dcm orig/00!

1213.dcm orig/001214.dcm orig/001215.dcm orig/001216.dcm orig/001217.dcm orig/ 001218.dcm orig/001219.dcm orig/001220.dcm orig/001221.dcm orig/ 001222.dcm 001.mgz

...

mri_convert: extra arguments ("orig/001090.dcm" and following)

Could anybody help me with this problem?

Thanks in advance, Gabriel

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