Hi Doety, Consider these options for uploading data: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
I think recon-all is expecting your wm.mgz to be conformed or 256^3. Something like: mri_convert wm.mgz wm.conform.mgz --conform
You would need to rename wm.conform.mgz to wm.mgz, after renaming or saving a copy of the current non-conformed wm mask you got from FSL. -Louis
On Thu, 10 Jul 2014, Doety Prins wrote:
Hi Bruce,
Thanks for your reply. In my previous e-mail I already tried to attach one of my subjects, but got the response that the message was too big, and therefore it was rejected. So how should I upload the image? The images are T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.
I discovered that FSL does a proper segmentation on this subjects, so I was looking for a way to import these segments from FSL into the Freesurfer pipeline, but I didn't succeed so far. I used the white matter segment from FSL as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol to get this segment in the right space, and normalized with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right size. Do you have any experience with this? Or any ideas about this?
Best regards,
Doety
On 9 jul. 2014, at 15:00, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Doety
yes, that looks pretty bad. Can you tell us about the acquisition? What resolution/field strength/scan type was it?
If you upload the subject we will take a look
cheers Bruce On Wed, 9 Jul 2014, Doety Prins wrote:
Dear freesurfer experts,
I experienced some problems with the segmentation of my T1 scans, as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies.
Do you have any solutions for this? Is it for instance possible to make changes to the recon-all script to shift the surfaces?
Thanks in advance,
Doety
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