Re: [Freesurfer] Problem with T1 Nifti file read {Disarmed}

You can try this one

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_convert.v53

On 03/06/2017 06:51 PM, Dhaval Shah wrote:

Could i get a solution for the earlier version than 6.0? I can't use the new one unfortunately.

On Mon, Mar 6, 2017 at 4:19 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

I think this problem is fixed in version 6. You can download version 6
and use the v6 mri_convert to convert the file. The converted file
should be readable by v5 (I think).


On 03/06/2017 04:14 PM, Dhaval Shah wrote:
> Hi Bruce,
>
> Thank you for your prompt e-mail. I have attached here the
recon-all.log.
>
> The mri_info command gives me the same error message as i mentioned
> before. Thank you for your help.
>
> On Mon, Mar 6, 2017 at 2:54 PM, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>
<mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>> wrote:
>
>     HI Dhaval
>
>     can you send us the full command line, screen output and
>     recon-all.log? Also: what does mri_info tell you when run on
that
>     file?
>
>     cheers
>     Bruce
>
>     On Mon, 6 Mar 2017, Dhaval Shah wrote:
>
>         Hi all,
>
>         i am having problem with recon-all function. Whenever i call
>         that function from a terminal
>         with my high resolution Nifti file ("MPRAGE.nii") it aborts
>         with an error: "nifti1Read():
>         unsupported slice Timing  pattern in ..."path to file".
>
>         Can some one please help? I need to generate Labels from
this
>         NIFTI file
>
>         --
>         Kind regards,
>         Dhaval Shah
>
>         MRI Research fellow,MRI Physicist,Clinical Trial
Research Staff
>         Buffalo Neuroimaging Analysis Center
>         State University of New York at Buffalo
>         Department of Neurology
>         100 High St., D-2, Buffalo, NY 14203
>         *MailScanner has detected a possible fraud attempt from
>         "dshah@bnac.net <mailto:dshah@bnac.net>" claiming to be*
*MailScanner has detected a
>         possible fraud attempt from "dshah@bnac.net
<mailto:dshah@bnac.net>" claiming to be*
> *MailScanner has detected a possible fraud attempt from
"dshah@bnac.net" claiming to be* *MailScanner has detected a
possible fraud attempt from "dshah@bnac.net" claiming to be*
dshah@bnac.net//http://mbl.bnac.net
<http://dshah@bnac.net//http://mbl.bnac.net>
>         <http://dshah@bnac.net//http://mbl.bnac.net
<http://dshah@bnac.net//http://mbl.bnac.net>>
>
>
>     _______________________________________________
>     Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>
>
>     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
<http://www.partners.org/complianceline>
>     <http://www.partners.org/complianceline
<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.
>
>
>
>
> --
> Kind regards,
> Dhaval Shah
> MRI Research fellow,MRI Physicist,Clinical Trial Research Staff
> Buffalo Neuroimaging Analysis Center State University of New York at
> Buffalo Department of Neurology 100 High St., D-2, Buffalo, NY 14203
> dshah@bnac.net <mailto:dshah@bnac.net> <mailto:dshah@bnac.net
<mailto:dshah@bnac.net>>//http://mbl.bnac.net <http://mbl.bnac.net>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>

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

-- Kind regards, Dhaval Shah MRI Research fellow,MRI Physicist,Clinical Trial Research Staff Buffalo Neuroimaging Analysis Center State University of New York at Buffalo Department of Neurology 100 High St., D-2, Buffalo, NY 14203 dshah@bnac.net mailto:dshah@bnac.net//http://mbl.bnac.net

---

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