can you try running this directly on a linux box? Or upload the .img/.hdr files and we will take a look

On Wed, 5 Oct 2011, m.vlutters wrote:

Thank you for the reply.

I do have the .hdr file, but calling just the hdr doesn't do any good.

"File not found or unknown filetype for ../.../ .hdr"

If I specify the input again with "-it spm" it gives:

"ERROR : analyzeRead(): cannot find any files for .../.../ .hdr"

First moving to the correct folder with "cd" doesn't help either.

I think I'll indeed try creating a nii file and see if I can convert the nii into mgz. No idea if that would work.

-----Original message----- From:Martijn Steenwijk martijnsteenwijk@gmail.com To:m.vlutters@atr.jp Cc:Freesurfer@nmr.mgh.harvard.edu Date:Wed, 5 Oct 2011 15:06:41 +0200 Subject:Re: [Freesurfer] .img unsupported data type ?

You might generate a hdr+img or nii file, and then specify the hdr or nii file to import from.

Best, Martijn

-----Oorspronkelijk bericht----- Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens m.vlutters Verzonden: woensdag 5 oktober 2011 7:27 Aan: freesurfer Onderwerp: [Freesurfer] .img unsupported data type ?

Dear FreeSurfers,

First of all, I am completely new to FS so forgive me if I missed something simple.

I am currently running freesurfer v5.1.0, using the .vdi file with VirtualBox. (Host = windows 7). I tested the program by running the autorecon1 on subject "bert" and everything seems to work fine so far.

Now I have a .img file (which I can view using SPM8), and I would like to convert it to a .mgz file using freesurfer's mri_convert. I tried the following:

mri_convert /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img /home/virtualuser/freesurfer/subjects/MySubj/001 -ot mgz

which gives me:

$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img... ReadAnalyzeHeader: unsupported data type 0

If I specify the input type as well (-it spm) I get:

$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img... ERROR: CountAnalyzeFiles: file with.img extension specified with zero pad variable.

I tried it with other .img files I have as well and I get similar errors. (Sometimes with a different number behind 'unsupported data type', like -12080)

What am I doing wrong? Does it have something to do with this zero pad variable? I don't expect the .img files to be wrong. They are generated by SPM8.

Thanks in advance for any replies!

Mark V _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Dear Freesurfers,

Bruce managed to convert the files on a Linux box. I will leave the virtualbox for what it is, get Linux installed and try it again.

Mark

-----Original message----- From:Douglas N Greve greve@nmr.mgh.harvard.edu To:m.vlutters@atr.jp Cc:Freesurfer Freesurfer@nmr.mgh.harvard.edu,martijnsteenwijk martijnsteenwijk@gmail.com Date:Wed, 05 Oct 2011 10:48:53 -0400 Subject:Re: [Freesurfer] .img unsupported data type ?

We don't have data type 0 defined in our code. Why are you using analyze at all? The field has moved on to nifti (for good reasons). Why not convert all your data to nifti? doug

m.vlutters wrote:

Thank you for the reply.

I do have the .hdr file, but calling just the hdr doesn't do any good.

"File not found or unknown filetype for ../.../ .hdr"

If I specify the input again with "-it spm" it gives:

"ERROR : analyzeRead(): cannot find any files for .../.../ .hdr"

First moving to the correct folder with "cd" doesn't help either.

I think I'll indeed try creating a nii file and see if I can convert the nii into mgz. No idea if that would work.

-----Original message----- From:Martijn Steenwijk martijnsteenwijk@gmail.com To:m.vlutters@atr.jp Cc:Freesurfer@nmr.mgh.harvard.edu Date:Wed, 5 Oct 2011 15:06:41 +0200 Subject:Re: [Freesurfer] .img unsupported data type ?

You might generate a hdr+img or nii file, and then specify the hdr or nii file to import from.

Best, Martijn

-----Oorspronkelijk bericht----- Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens m.vlutters Verzonden: woensdag 5 oktober 2011 7:27 Aan: freesurfer Onderwerp: [Freesurfer] .img unsupported data type ?

Dear FreeSurfers,

First of all, I am completely new to FS so forgive me if I missed something simple.

I am currently running freesurfer v5.1.0, using the .vdi file with VirtualBox. (Host = windows 7). I tested the program by running the autorecon1 on subject "bert" and everything seems to work fine so far.

Now I have a .img file (which I can view using SPM8), and I would like to convert it to a .mgz file using freesurfer's mri_convert. I tried the following:

mri_convert /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img /home/virtualuser/freesurfer/subjects/MySubj/001 -ot mgz

which gives me:

$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img... ReadAnalyzeHeader: unsupported data type 0

If I specify the input type as well (-it spm) I get:

$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/MySubj/NS-3D.img... ERROR: CountAnalyzeFiles: file with.img extension specified with zero pad variable.

I tried it with other .img files I have as well and I get similar errors. (Sometimes with a different number behind 'unsupported data type', like -12080)

What am I doing wrong? Does it have something to do with this zero pad variable? I don't expect the .img files to be wrong. They are generated by SPM8.

Thanks in advance for any replies!

Mark V _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Glad it worked out, but try to avoid analyze if you can!

Cheers Bruce

On Oct 11, 2011, at 9:44 PM, "m.vlutters" m.vlutters@atr.jp wrote:

I tried converting and recon-all using Freesurfer on a Linux installation and it works fine.

I have no idea what went wrong with the virtualbox, but it works for me now.

All thanks for the help :) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer