Hi Bruce,

Thanks for your response. It's a bit of a pain to access the dicoms, but it's possible. The bigger problem now is that I can't get freeview to work. I type in freeview into the command line and receive the following error:

freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory

Forgive my lack of linux knowledge, but is there some software I failed to download? I searched for the error in the Mail Archive and the only entry is from April 7, 2011. The response to the query says something about glxgear. Is that something I should try to get freeview running? If so, how do I do that?

As a side note, tksurfer and tkmedit seem to work fine.

Jared

On Dec 12, 2013, at 3:36 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Jared

for the ones that run quickly and end, it's because you haven't told it to do anything. The first couple of lines of the recon-all.log file give the command line as:

Thu Dec 5 14:00:18 MST 2013 /mnt/NAS3/freesurfer/freesurfer//bin/recon-all -i Time3_28908_s11038064-0005-00001-000001-01.nii -subject Time3_28908

this will just convert the nifti and create the subject dirs for Time3_28908. You need to add "-all" at the end of the line, as you did in the other ones.

For the one that failed the talairach it's hard to say. You are starting with nifti - can you try it directly on the dicoms? Where did you get the nifti from? If you bring the nifti input volume up in freeview does it show in the correct orientation? That is, is what freeview thinks is anterior truly anterior, etc....?

cheers Bruce

On Thu, 12 Dec 2013, JARED NIELSEN wrote:

...

Hi,

I'm new to FreeSurfer and have been going through the tutorials, YouTube videos, and Mail Archive. I've run recon-all on a handful of scans with variable success. Some of the scans are processed after five or six hours without any problems, and the output looks good. Others are processed "without any errors" after a matter of minutes, and logically I don't see any output. Finally, others hit a hard error after a few minutes of processing during the talairach transformation step. I looked at the orig.mgz file (for the scan that failed at transformation step) through tkmedit, and it is a blank white rectangle. I don't see anything that resembles a head or brain. I've attached examples of each recon-all.log (i.e., good, bad, and bad_talairach). Any help would be greatly appreciated.

Thanks, Jared

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It could be that SPM is setting some scaling factor in the nifti header that FS is not reading properly. Which version of FS are you using? doug

On 12/17/2013 02:38 PM, JARED NIELSEN wrote:

I looked at the nifti files in freeview. The orientation in freeview is correct, but it appears all of the T1s that resulted in an error are washed out in freeview. I can vaguely see the outline of the head, but there's a gray box covering the image. When I click on regions of bone or brain in the washed out images, the intensities are comparable with those of non-washed out images.

I created the nifti files using spm. When I display the nifti files in afni or spm they look great. Is there something about the spm-generated nifti files that freesurfer doesn't like? Should I use a different program to convert the dicoms into niftis?

I also went back to the original dicoms. If I generate the 001.mgz file from the dicoms, recon-all works appropriately and the image is not washed out. I could always go back and work with the dicoms directly, but moving forward I would prefer working with the nifti files for protected health information reasons.

Thanks, Jared

On Dec 12, 2013, at 4:56 PM, Jared Nielsen jared.nielsen@hsc.utah.edu wrote:

...

Hi Bruce,

Thanks for your response. It's a bit of a pain to access the dicoms, but it's possible. The bigger problem now is that I can't get freeview to work. I type in freeview into the command line and receive the following error:

freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory

Forgive my lack of linux knowledge, but is there some software I failed to download? I searched for the error in the Mail Archive and the only entry is from April 7, 2011. The response to the query says something about glxgear. Is that something I should try to get freeview running? If so, how do I do that?

As a side note, tksurfer and tkmedit seem to work fine.

Jared

On Dec 12, 2013, at 3:36 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Jared

for the ones that run quickly and end, it's because you haven't told it to do anything. The first couple of lines of the recon-all.log file give the command line as:

Thu Dec 5 14:00:18 MST 2013 /mnt/NAS3/freesurfer/freesurfer//bin/recon-all -i Time3_28908_s11038064-0005-00001-000001-01.nii -subject Time3_28908

this will just convert the nifti and create the subject dirs for Time3_28908. You need to add "-all" at the end of the line, as you did in the other ones.

For the one that failed the talairach it's hard to say. You are starting with nifti - can you try it directly on the dicoms? Where did you get the nifti from? If you bring the nifti input volume up in freeview does it show in the correct orientation? That is, is what freeview thinks is anterior truly anterior, etc....?

cheers Bruce

On Thu, 12 Dec 2013, JARED NIELSEN wrote:

...

Hi,

I'm new to FreeSurfer and have been going through the tutorials, YouTube videos, and Mail Archive. I've run recon-all on a handful of scans with variable success. Some of the scans are processed after five or six hours without any problems, and the output looks good. Others are processed "without any errors" after a matter of minutes, and logically I don't see any output. Finally, others hit a hard error after a few minutes of processing during the talairach transformation step. I looked at the orig.mgz file (for the scan that failed at transformation step) through tkmedit, and it is a blank white rectangle. I don't see anything that resembles a head or brain. I've attached examples of each recon-all.log (i.e., good, bad, and bad_talairach). Any help would be greatly appreciated.

Thanks, Jared

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.

---

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