Hi Dr. Greve, Thank you very much for getting back to me so promptly. If memory serves me right, I am pretty sure that the orientations were incorrect in tkmedit but will double check soon. Based on what you are saying and based on what I read in the wiki about mri_convert it seems that I will be able to change all of my nifti files using mri_convert and then I can use the newly generated niftis to run reconall? Is this correct?
As I am very new to FS, I don't know what it means to give it an orientation string? Is there some documentation where I can look this up further? In any case, thank you very much and I will keep you posted! Best, Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayak...@student.gsu.edu Message: 24 > Date: Tue, 22 Mar 2016 10:56:40 -0400 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1 > qform or sform are valid > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <56f15d28.7040...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > To check whether the orientation is correct, you can view it in freeview > or tkmedit. When you click on the axial view it should show up axially, > etc. Though you cannot tell whether it is left-right reversed this way. > You cannot feed it a matrix, but you can specify the direction cosines > on the mri_convert command line (-iid, -ijd, -ikd). You'll have to play > with it a bit. You can also try giving it an orientation string instead. > if you run mri_convert without any options, then it will give you lots > of documentation. > > On 3/20/16 8:44 PM, Reema Jayakar wrote: > > Hello FS list subscribers, > > > > Is there a way to manually feed FS with NIfTI-1 qform or sform > > information? Or correctly add this information to the original .nii > > files? My sense of the problem is that there is a problem with the > > header information in my .nii files and FS cannot tell what is > > anterior, posterior, left, right. > > > > That said, I am very new to FS and my interpretation of the error > > could be wrong. So I am laying out the details below (recon-all.log is > > also attached to this email): > > > > * When I try to run recon-all there are no output images/files > > generated and the message I get is that the Talairach transform > > failed > > * When I try to run autorecon1 an autorecon2 with the "-notal check" > > flag, FS does not give me any error message and proceeds with > > generating output. However, I can visually see (via brainmask.mgz) > > that oreintations are messed up (e.g., tried to register coronal > > orientation on top of sagittal orientation) > > * This problem only occurs with .nii files from a particular study > > that came out of a specific scanner. All my other data are running > > through FS smoothly, which is why I think there is some problem > > with the .nii files > > * Also, when I view my raw .nii images in FSL view none of the usual > > orientation markers are visible to me, which again suggest that > > they may be missing? > > * Unfortunately, I do not currently have the original .dcm files > > available as this is a multi-site archival study > > > > > > Any help you can provide to resolve this issue would be really > > appreciated! > > > > Thank you, > > Reema > > > > > > > > -- > > *Reema Jayakar, M.A.* > > Doctoral Candidate - Clinical Neuropsychology > > Health Resources and Services Administration (HRSA) Fellow > > Department of Psychology > > Georgia State University > > Email: rjayak...@student.gsu.edu <mailto:rjayak...@student.gsu.edu> > ******************************************* >
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