Re: [Freesurfer] Multiple inputs into recon-all -i

[ye tian]

Dear Bruce,

Thank you very much!

Sincerely,
Ye


On Mon, Jun 24, 2013 at 7:32 PM, Bruce Fischl wrote:

> Hi Ye,
>
> you would never have two files, as each file represents one image, or
> slice from a sequence. So you might have two  sequences of files, say
> Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima,
> Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once with
> *one* file from each series (it wouldn't matter which one).
>
>
> cheers
> Bruce
>
> On Mon, 24 Jun 2013, ye tian wrote:
>
>  Dear Bruce,
>> Thank you very much for your suggestion, but I am afraid that I still
>> don't
>> quite understand you.
>>
>> In order to make it simple, suppose I have two files, Barba001.IMA and
>> Barba002.IMA, coming directly from the scanner.
>>
>> Now if I enter  recon-all -s Barba -i Barba001.IMA  from the command
>> line, I
>> am only able to find   001.mgz  in the Barba/mri/orig. Aren't I supposed
>> to
>> to find 001.mgz and 002.mgz?
>>
>> Thank you so much!
>>
>> Sincerely,
>> Ye
>>
>>
>> On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl > >
>> wrote:
>>   Hi Ye
>>
>>   you only need to give it a single file from each run and it will
>>   find the rest. The only time you use -i more than once is if you
>>   acquired more than 1 T1-weighted volume. Definitely don't give
>>   it all the files that make up the same volume
>>
>>   cheers
>>   Bruce
>>   On Mon, 24 Jun 2013, ye tian wrote:
>>
>> Dear David,
>> I wonder whether there is a short cut for recon-all
>> -s Barbara -i
>> /path_to_data/scan1.dicom -i
>> /path_to_data/scan2.dicom ... -i
>> /path_to_data/scan100.dicom
>>
>> Recon-all -i takes only a single file as an input. A
>> typical user, however,
>> has hundreds of files for a particular subject. For
>> example, the directory
>> Barbara may have 100 scans. Therefore, the above
>> command is necessary to
>> include all the scans.
>>
>> I understand that I can write loops to a text file
>> and then copy and paste
>> to command line. However, I wonder whether there is
>> a simpler way to input
>> several files or even a directory to recon-all.
>>
>> Thank you very much!
>>
>> Sincerely,
>> Ye
>>
>>
>>
>>
>> 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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Re: [Freesurfer] Multiple inputs into recon-all -i

[Bruce Fischl]

Hi Ye,

you would never have two files, as each file represents one image, or 
slice from a sequence. So you might have two  sequences of files, say 
Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima, 
Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once with 
*one* file from each series (it wouldn't matter which one).


cheers
Bruce

On 
Mon, 24 Jun 2013, ye tian wrote:



Dear Bruce,
Thank you very much for your suggestion, but I am afraid that I still don't
quite understand you.

In order to make it simple, suppose I have two files, Barba001.IMA and
Barba002.IMA, coming directly from the scanner.

Now if I enter  recon-all -s Barba -i Barba001.IMA  from the command line, I
am only able to find   001.mgz  in the Barba/mri/orig. Aren't I supposed to
to find 001.mgz and 002.mgz?

Thank you so much!

Sincerely,
Ye


On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl 
wrote:
  Hi Ye

  you only need to give it a single file from each run and it will
  find the rest. The only time you use -i more than once is if you
  acquired more than 1 T1-weighted volume. Definitely don't give
  it all the files that make up the same volume

  cheers
  Bruce
  On Mon, 24 Jun 2013, ye tian wrote:

Dear David,
I wonder whether there is a short cut for recon-all
-s Barbara -i
/path_to_data/scan1.dicom -i
/path_to_data/scan2.dicom ... -i
/path_to_data/scan100.dicom 

Recon-all -i takes only a single file as an input. A
typical user, however,
has hundreds of files for a particular subject. For
example, the directory
Barbara may have 100 scans. Therefore, the above
command is necessary to
include all the scans. 

I understand that I can write loops to a text file
and then copy and paste
to command line. However, I wonder whether there is
a simpler way to input
several files or even a directory to recon-all.

Thank you very much!

Sincerely,
Ye




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
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but does not contain patient information, please contact the sender
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Re: [Freesurfer] Multiple inputs into recon-all -i

[ye tian]

Dear Bruce,

Thank you very much for your suggestion, but I am afraid that I still don't
quite understand you.

In order to make it simple, suppose I have two files, Barba001.IMA and
Barba002.IMA, coming directly from the scanner.

Now if I enter  *recon-all -s Barba -i Barba001.IMA*  from the command
line, I am only able to find   *001.mgz*  in the Barba/mri/orig. Aren't I
supposed to to find 001.mgz and 002.mgz?

Thank you so much!

Sincerely,
Ye


On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl wrote:

> Hi Ye
>
> you only need to give it a single file from each run and it will find the
> rest. The only time you use -i more than once is if you acquired more than
> 1 T1-weighted volume. Definitely don't give it all the files that make up
> the same volume
>
> cheers
> Bruce
>
> On Mon, 24 Jun 2013, ye tian wrote:
>
>  Dear David,
>> I wonder whether there is a short cut for recon-all -s Barbara -i
>> /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i
>> /path_to_data/scan100.dicom
>>
>> Recon-all -i takes only a single file as an input. A typical user,
>> however,
>> has hundreds of files for a particular subject. For example, the directory
>> Barbara may have 100 scans. Therefore, the above command is necessary to
>> include all the scans.
>>
>> I understand that I can write loops to a text file and then copy and paste
>> to command line. However, I wonder whether there is a simpler way to input
>> several files or even a directory to recon-all.
>>
>> Thank you very much!
>>
>> Sincerely,
>> Ye
>>
>>
>>
>
> 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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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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dispose of the e-mail.

Re: [Freesurfer] Multiple inputs into recon-all -i

[Bruce Fischl]

Hi Ye

you only need to give it a single file from each run and it will find the 
rest. The only time you use -i more than once is if you acquired more 
than 1 T1-weighted volume. Definitely don't give it all the files that 
make up the same volume


cheers
Bruce
On Mon, 24 Jun 2013, ye tian wrote:


Dear David,
I wonder whether there is a short cut for recon-all -s Barbara -i
/path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i
/path_to_data/scan100.dicom 

Recon-all -i takes only a single file as an input. A typical user, however,
has hundreds of files for a particular subject. For example, the directory
Barbara may have 100 scans. Therefore, the above command is necessary to
include all the scans. 

I understand that I can write loops to a text file and then copy and paste
to command line. However, I wonder whether there is a simpler way to input
several files or even a directory to recon-all.

Thank you very much!

Sincerely,
Ye

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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] Multiple inputs into recon-all -i

[ye tian]

Dear David,

I wonder whether there is a short cut for recon-all -s Barbara -i
/path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i
/path_to_data/scan100.dicom

Recon-all -i takes only a single file as an input. A typical user, however,
has hundreds of files for a particular subject. For example, the directory
Barbara may have 100 scans. Therefore, the above command is necessary to
include all the scans.

I understand that I can write loops to a text file and then copy and paste
to command line. However, I wonder whether there is a simpler way to input
several files or even a directory to recon-all.

Thank you very much!

Sincerely,
Ye
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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.