Hello Mr.Schrader,

Is is the "avant" folder saved in the path/folder from where you are runnning this command?

 

Thanks.

 

On 7/12/07, Birte Schrader <birte@ethz.ch> wrote:

Hi Bruce,

 

thanks for replying so fast. But somehow I still don't get this running. When I say:

 

"mri_convert avant/IM-0001-0001.dcm avant.mgz"

 

I get:

 

"mri_convert avant/IM-0001-0001.dcm avant.mgz

unknown file type for file avant/IM-0001-0001.dcm"

 

when saying:

 

"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz"

 

I get:

 

"mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz

reading from avant/IM-0001-0001.dcm...

no DICOM files found. Exit"

 

I don't have any idea what's wrong there.

 

Cheers,

Birte

 

 

 

 

On Jul 12, 2007, at 9:02 PM, Bruce Fischl wrote:

 

Hi Birte,

you need to specify the name of a single DICOM file that is in the series you want to use for building anatomical models, not just the directory name.

cheers,

Bruce

On Thu, 12 Jul 2007, Birte Schrader wrote:

Hello,

I just downloaded and installed the freesurfer and got up the step where I tested it by trying "recon-all -s bert -autorecon1". This works fine :-)

Now I (thoroughly) followed the instructions "Getting started with your own data" in of https://surfer.nmr.mgh.harvard.edu/fswiki/ TestingFreeSurfer. But unfortunately the mri_convert command does not work on (my?) dicom-files:

"mri_convert -it dicom -ot mgz avant/ avant.mgz"

is what I type in. I am really in mri/orig/ and in mri/orig/avant are 120 .dcm-files so I don't see what's wrong. I get the error message:

"reading from avant/...

no DICOM files found. Exit"

Do you know if there are different types if dicom-files and not all of them are supported? Or do you see anything else that might be wrong?

Thanks in advance.

Birte

PS: The FreeSurfer software was highly recommended to me by a friend of a friend of mine, so I am really looking forward to trying it on my data...

PPS: tkmedit and tksurfer do not work yet for me. But that is some problem with displaying the windows. I get "GLUT: Fatal Error in tksurfer.bin: could not open display:". But this shouldn't alter the no-display-functions of freesurfer, no? Visualization I can do otherwise if I cannot fix it...

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