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
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 dshah@bnac.net//http://mbl.bnac.net
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 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 dshah@bnac.net//http://mbl.bnac.net
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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> 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" 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> _______________________________________________ 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> 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> . 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//http://mbl.bnac.net
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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 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> 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" 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> _______________________________________________ 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> 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> . 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//http://mbl.bnac.net
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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why not? YOu don't need all of 6 - just mri_convert. You can rename it mri_convert.v6 if you want so you don't overwrite the older one On Mon, 6 Mar 2017, 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 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>> 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" 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 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
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-- 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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- 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//http://mbl.bnac.net
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
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