What's your cmd line and what exactly is the problem?

doug

Hi, the commands and problems are pasted below.

Thanks,

Anders

[brain@striatum folder]# cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 [brain@striatum folder]#

[brain@striatum raw]# mri_convert -i 12461.spgr -o 12461.mgz mri_convert -i 12461.spgr -o 12461.mgz file not found or unknown file type for file 12461.spgr

[brain@striatum raw]# mri_convert -it ge -i 12461.spgr -ot mgz -o 12461.mgz mri_convert -it ge -i 12461.spgr -ot mgz -o 12461.mgz $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from 12461.spgr... genesisRead(): can't determine file name format for /usit/psi-brain/u1/Felles/labdata/lab-data/multisample/folder/raw/12461.spgr

[brain@striatum raw]# mri_info 12461.spgr ERROR: could not determine type of 12461.spgr

We have also tried to replace -it ge with gelx, ximg, and brik, with the same result.

a.m.fjell@psykologi.uio.no wrote:

...

Hi, we have problems converting scans obtained from a GE scanner with a T1-weighted 3-D spoiled gradient recalled (SPGR) sequence to anything freesurfer can read.

Any tips?

Thanks!

• Anders

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Is it a dicom? Try

mri_convert -i 12461.spgr -o 12461.mgz -it dicom

It did not work either, unfortunately.

- Anders

doug

a.m.fjell@psykologi.uio.no wrote:

...

...

What's your cmd line and what exactly is the problem?

doug

Hi, the commands and problems are pasted below.

Thanks,

Anders

[brain@striatum folder]# cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 [brain@striatum folder]#

[brain@striatum raw]# mri_convert -i 12461.spgr -o 12461.mgz mri_convert -i 12461.spgr -o 12461.mgz file not found or unknown file type for file 12461.spgr

[brain@striatum raw]# mri_convert -it ge -i 12461.spgr -ot mgz -o 12461.mgz mri_convert -it ge -i 12461.spgr -ot mgz -o 12461.mgz $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from 12461.spgr... genesisRead(): can't determine file name format for /usit/psi-brain/u1/Felles/labdata/lab-data/multisample/folder/raw/12461.spgr

[brain@striatum raw]# mri_info 12461.spgr ERROR: could not determine type of 12461.spgr

We have also tried to replace -it ge with gelx, ximg, and brik, with the same result.

...

a.m.fjell@psykologi.uio.no wrote:

...

Hi, we have problems converting scans obtained from a GE scanner with a T1-weighted 3-D spoiled gradient recalled (SPGR) sequence to anything freesurfer can read.

Any tips?

Thanks!

• Anders

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

you might try -it ge or -it gelx

Thanks for the tips. We have tried both without luck, unfortunately.

- Anders

doug

a.m.fjell@psykologi.uio.no wrote:

...

...

Is it a dicom? Try

mri_convert -i 12461.spgr -o 12461.mgz -it dicom

It did not work either, unfortunately.

• Anders

...

doug

a.m.fjell@psykologi.uio.no wrote:

...

...

What's your cmd line and what exactly is the problem?

doug

Hi, the commands and problems are pasted below.

Thanks,

Anders

[brain@striatum folder]# cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 [brain@striatum folder]#

[brain@striatum raw]# mri_convert -i 12461.spgr -o 12461.mgz mri_convert -i 12461.spgr -o 12461.mgz file not found or unknown file type for file 12461.spgr

[brain@striatum raw]# mri_convert -it ge -i 12461.spgr -ot mgz -o 12461.mgz mri_convert -it ge -i 12461.spgr -ot mgz -o 12461.mgz $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from 12461.spgr... genesisRead(): can't determine file name format for /usit/psi-brain/u1/Felles/labdata/lab-data/multisample/folder/raw/12461.spgr

[brain@striatum raw]# mri_info 12461.spgr ERROR: could not determine type of 12461.spgr

We have also tried to replace -it ge with gelx, ximg, and brik, with the same result.

...

a.m.fjell@psykologi.uio.no wrote:

...

Hi, we have problems converting scans obtained from a GE scanner with a T1-weighted 3-D spoiled gradient recalled (SPGR) sequence to anything freesurfer can read.

Any tips?

Thanks!

• Anders

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting