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: rjayakar1@student.gsu.edu

Message: 24
Date: Tue, 22 Mar 2016 10:56:40 -0400
From: Douglas Greve <greve@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: <56F15D28.7040207@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: rjayakar1@student.gsu.edu <mailto:rjayakar1@student.gsu.edu>
*******************************************

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