Dear All,
I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command:
mri_convert -i name_of_input_file -it analyze -ot nii -o name_of_output_file
But the output file has not proper nii format, When I drag the file in the MRIcro I just see a single slice with scrambled picture. It is appreciated if anybody could help me and let me know which switches I should use.
Thanks,
Fari
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can you give us your actual command line? It should be something like
mri_convert file.img file.nii
On 1/20/16 11:14 PM, Mahmoudi, Fariborz wrote:
Dear All,
I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command:
mri_convert -i/name_of_input_file/-it/analyze /-ot/nii/-o /name_of_output_file/
But the output file has not proper nii format, When I drag the file in the MRIcro I just see a single slice with scrambled picture. It is appreciated if anybody could help me and let me know which switches I should use.
Thanks,
Fari
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Hi Fari
we need the full command line and screen output in order to help you.
cheers Bruce On Thu, 21 Jan 2016, Mahmoudi, Fariborz wrote:
Dear All,
I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command:
mri_convert -i name_of_input_file -it analyze -ot nii -o name_of_output_file
But the output file has not proper nii format, When I drag the file in the MRIcro I just see a single slice with scrambled picture. It is appreciated if anybody could help me and let me know which switches I should use.
Thanks,
Fari
CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.
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Hi Bruce,
The problem is solved by adding .img extension to input file name, but I have a new problem. The origin of the output file is not zero. Is there any switch for tuning the origin. My actual command line is:
/usr/local/freesurfer/bin/mri_convert -i ./FLAIR_Sample.img -it analyze -ot nii -o FLAIR_Sample.nii
Thanks, Fari
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Thursday, January 21, 2016 8:56 AM To: Freesurfer support list Subject: Re: [Freesurfer] Analyze to nii convertor
Hi Fari
we need the full command line and screen output in order to help you.
cheers Bruce On Thu, 21 Jan 2016, Mahmoudi, Fariborz wrote:
Dear All,
I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command:
mri_convert -i name_of_input_file -it analyze -ot nii -o name_of_output_file
But the output file has not proper nii format, When I drag the file in the MRIcro I just see a single slice with scrambled picture. It is appreciated if anybody could help me and let me know which switches I should use.
Thanks,
Fari
CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.
Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.
No, try FSL
On 01/21/2016 10:08 AM, Mahmoudi, Fariborz wrote:
Hi Bruce,
The problem is solved by adding .img extension to input file name, but I have a new problem. The origin of the output file is not zero. Is there any switch for tuning the origin. My actual command line is:
/usr/local/freesurfer/bin/mri_convert -i ./FLAIR_Sample.img -it analyze -ot nii -o FLAIR_Sample.nii
Thanks, Fari
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Thursday, January 21, 2016 8:56 AM To: Freesurfer support list Subject: Re: [Freesurfer] Analyze to nii convertor
Hi Fari
we need the full command line and screen output in order to help you.
cheers Bruce On Thu, 21 Jan 2016, Mahmoudi, Fariborz wrote:
Dear All,
I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command:
mri_convert -i name_of_input_file -it analyze -ot nii -o name_of_output_file
But the output file has not proper nii format, When I drag the file in the MRIcro I just see a single slice with scrambled picture. It is appreciated if anybody could help me and let me know which switches I should use.
Thanks,
Fari
CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies.
Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve
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Mahmoudi, Fariborz