Re: [Freesurfer] convert nii to nii.gz

[Ting Li]

Dear Bruce,

Thanks for your response. I will check it today.

Best,
Ting
> On Jan 21, 2018, at 10:41 AM, Bruce Fischl  wrote:
> 
> Hi Ting
> 
> if you can't see the share folder then you can't access our binaries. Maybe 
> talk to your local sysadmins?
> 
> cheers
> Bruce
> On Sat, 20 Jan 2018, Ting Li wrote:
> 
>> Hi Bruce,
>> Thanks for your quickly response. Sorry for my late.
>> I try to run FreeSurfer in a server. It was installed in my home share 
>> folder. Here is the setting
>> environment information. 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /home/share/freesurfer
>> FSFAST_HOME   /home/share/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  /home/share/freesurfer/subjects
>> MNI_DIR   /home/share/freesurfer/mni
>> And I defined my SUBJECTS_DIR is /home/ting/freesurfer_subjects_data.
>> When I do a ls,  I can’t see the share folder. Do you think I should install 
>> if
>> under /home/ting instead of /home/share?
>> Thanks a lot!
>> Best,
>> Ting
>> On Jan 20, 2018, at 9:12 AM, Bruce Fischl  wrote:
>> 
>>  Hi Ting
>> 
>>  that means $FREESURFER_HOME/bin is not in your path and you need to add 
>> it
>>  (and make sure that the environment variable FREESURFER_HOME is set
>>  properly). If it is, you can do:
>> 
>>  source $FREESURFER_HOME/SetUpFreeSurfer.csh
>> 
>>  Are you new to Linux also?  If so, you might want to go through some 
>> basic
>>  tutorials.
>> 
>>  cheers
>>  Bruce
>> 
>>  On Fri, 19 Jan 2018, Ting Li wrote:
>> 
>>Hi Freesurfer Expert,
>> 
>>I am very new to Freesurfer and have a very basic question. How 
>> to convert
>>.nii files to nii.gz? I have tried the mri_convert 
>> subject_name.nii to
>>subject_name.nii.gz directly. It gives me an error information 
>> that
>>mri_convert: command not found. Thanks for your help!
>> 
>>Best,
>>Ting
>> 
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>> 
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>> e-mail
>>  contains patient information, please contact the Partners Compliance 
>> HelpLine at
>>  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.
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> 
> 
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> 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 . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
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Re: [Freesurfer] convert nii to nii.gz

[Bruce Fischl]

Hi Ting

if you can't see the share folder then you can't access our binaries. 
Maybe talk to your local sysadmins?


cheers
Bruce
On Sat, 20 Jan 2018, Ting Li wrote:


Hi Bruce,
Thanks for your quickly response. Sorry for my late.

I try to run FreeSurfer in a server. It was installed in my home share folder. 
Here is the setting
environment information. 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/share/freesurfer
FSFAST_HOME       /home/share/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /home/share/freesurfer/subjects
MNI_DIR           /home/share/freesurfer/mni

And I defined my SUBJECTS_DIR is /home/ting/freesurfer_subjects_data.
When I do a ls,  I can’t see the share folder. Do you think I should install if
under /home/ting instead of /home/share?

Thanks a lot!

Best,
Ting

On Jan 20, 2018, at 9:12 AM, Bruce Fischl  wrote:

  Hi Ting

  that means $FREESURFER_HOME/bin is not in your path and you need to add it
  (and make sure that the environment variable FREESURFER_HOME is set
  properly). If it is, you can do:

  source $FREESURFER_HOME/SetUpFreeSurfer.csh

  Are you new to Linux also?  If so, you might want to go through some basic
  tutorials.

  cheers
  Bruce

  On Fri, 19 Jan 2018, Ting Li wrote:

Hi Freesurfer Expert,

I am very new to Freesurfer and have a very basic question. How to 
convert
.nii files to nii.gz? I have tried the mri_convert subject_name.nii 
to
subject_name.nii.gz directly. It gives me an error information that
mri_convert: command not found. Thanks for your help!

Best,
Ting



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  ___
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  Freesurfer@nmr.mgh.harvard.edu
  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 . 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.



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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] convert nii to nii.gz

[Ting Li]

Hi Bruce,

Thanks for your quickly response. Sorry for my late.

I try to run FreeSurfer in a server. It was installed in my home share folder. 
Here is the setting environment information. 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/share/freesurfer
FSFAST_HOME   /home/share/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/share/freesurfer/subjects
MNI_DIR   /home/share/freesurfer/mni

And I defined my SUBJECTS_DIR is /home/ting/freesurfer_subjects_data.
When I do a ls,  I can’t see the share folder. Do you think I should install if 
under /home/ting instead of /home/share?

Thanks a lot!

Best,
Ting

On Jan 20, 2018, at 9:12 AM, Bruce Fischl  wrote:
> 
> 
> Hi Ting
> 
> that means $FREESURFER_HOME/bin is not in your path and you need to add it 
> (and make sure that the environment variable FREESURFER_HOME is set 
> properly). If it is, you can do:
> 
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
> 
> Are you new to Linux also?  If so, you might want to go through some basic 
> tutorials.
> 
> cheers
> Bruce
> 
> On Fri, 19 Jan 2018, Ting Li wrote:
> 
>> Hi Freesurfer Expert,
>> 
>> I am very new to Freesurfer and have a very basic question. How to convert 
>> .nii files to nii.gz? I have tried the mri_convert subject_name.nii to 
>> subject_name.nii.gz directly. It gives me an error information that 
>> mri_convert: command not found. Thanks for your help!
>> 
>> Best,
>> Ting
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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 . 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.
> 

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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 . 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.

Re: [Freesurfer] convert nii to nii.gz

[Bruce Fischl]

Hi Ting

that means $FREESURFER_HOME/bin is not in your path and you need to add it 
(and make sure that the environment variable FREESURFER_HOME is set 
properly). If it is, you can do:

source $FREESURFER_HOME/SetUpFreeSurfer.csh

Are you new to Linux also?  If so, you might want to go through some basic 
tutorials.

cheers
Bruce

On Fri, 19 Jan 2018, Ting Li wrote:

> Hi Freesurfer Expert,
>
> I am very new to Freesurfer and have a very basic question. How to convert 
> .nii files to nii.gz? I have tried the mri_convert subject_name.nii to 
> subject_name.nii.gz directly. It gives me an error information that 
> mri_convert: command not found. Thanks for your help!
>
> Best,
> Ting
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
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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 . 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.

[Freesurfer] convert nii to nii.gz

[Ting Li]

Hi Freesurfer Expert, 

I am very new to Freesurfer and have a very basic question. How to convert .nii 
files to nii.gz? I have tried the mri_convert subject_name.nii to 
subject_name.nii.gz directly. It gives me an error information that 
mri_convert: command not found. Thanks for your help!

Best,
Ting 



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Freesurfer@nmr.mgh.harvard.edu
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 . 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.