run recon all with forced orientation, spacing and dimension

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Re: [Freesurfer] V6 Stable OSX...

Ritesh Mahajan

10 May 2018 10 May '18

4:14 a.m.

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Hello Team,

As i know free-surfer generates the output with following: 1) Dimensions : 256*256*256 2) Spacing : 1, 1,1 mm 3) Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

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Bruce Fischl

10 May 10 May

9:49 a.m.

New subject: run recon all with forced orientation, spacing and dimension

Hi Ritesh

no, not really. What is your goal? We should handle any input orientation as long as it is specified in the headers.

cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote:

...

   External Email - Use Caution
Hello Team,

As i know free-surfer generates the output with following:

Dimensions : 256*256*256

Spacing : 1, 1,1 mm

Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

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

Ritesh Mahajan

10:51 a.m.

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Thank you Bruse. Actually i converted the input into RAI orientation using mri_convert --out_orientation and gave RAI input the free-surfer through recon-all. The results are not generated.

My goal is to run free-surfer with RAI orientation and result should be in RAI. I also want the output of free-surfer with dimensions as 128*128*128 and spacing as 2,2,2 mm.

Can you tell whether this can be done using free-surfer?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Ritesh Mahajan" ritesh.mahajan@ripl.ricoh.com To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 1:44:40 PM Subject: run recon all with forced orientation, spacing and dimension

External Email - Use Caution

Hello Team,

As i know free-surfer generates the output with following: 1) Dimensions : 256*256*256 2) Spacing : 1, 1,1 mm 3) Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

_______________________________________________ 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.

Bruce Fischl

10:52 a.m.

New subject: run recon all with forced orientation, spacing and dimension

Hi Ritesh

your best bet is to run everything normally, then convert the output to whatever format/orientation/voxel size you want

cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote:

...

   External Email - Use Caution
Thank you Bruse. Actually i converted the input into RAI orientation using mri_convert --out_orientation and gave RAI input the free-surfer through recon-all. The results are not generated.

My goal is to run free-surfer with RAI orientation and result should be in RAI. I also want the output of free-surfer with dimensions as 128*128*128 and spacing as 2,2,2 mm.

Can you tell whether this can be done using free-surfer?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Ritesh Mahajan" ritesh.mahajan@ripl.ricoh.com To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 1:44:40 PM Subject: run recon all with forced orientation, spacing and dimension

External Email - Use Caution

Hello Team,

As i know free-surfer generates the output with following:

Dimensions : 256*256*256

Spacing : 1, 1,1 mm

Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

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.

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

Ritesh Mahajan

11:59 a.m.

New subject: run recon all with forced orientation, spacing and dimension

External Email - Use Caution

Hi Bruce,

Thanks Bruce i understand that.

But can't i run free-surfer with all these parameters (size, spacing and orientation) ?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 8:22:38 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh

your best bet is to run everything normally, then convert the output to whatever format/orientation/voxel size you want

cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote:

...

   External Email - Use Caution
Thank you Bruse. Actually i converted the input into RAI orientation using mri_convert --out_orientation and gave RAI input the free-surfer through recon-all. The results are not generated.

My goal is to run free-surfer with RAI orientation and result should be in RAI. I also want the output of free-surfer with dimensions as 128*128*128 and spacing as 2,2,2 mm.

Can you tell whether this can be done using free-surfer?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Ritesh Mahajan" ritesh.mahajan@ripl.ricoh.com To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 1:44:40 PM Subject: run recon all with forced orientation, spacing and dimension

External Email - Use Caution

Hello Team,

As i know free-surfer generates the output with following:

Dimensions : 256*256*256

Spacing : 1, 1,1 mm

Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

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.

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

Bruce Fischl

12:20 p.m.

New subject: run recon all with forced orientation, spacing and dimension

because internally we expect things to be a certain way (which is why we convert the data to that format). There are also some requirements on the data that you have to meet. For example 2mm is not high enough resolution to get accurate cortical models. The acquired data has to be no bigger than about 1.5mm in any dimension.

cheers Bruce

On Thu, 10 May 2018, Ritesh Mahajan wrote:

...

   External Email - Use Caution
Hi Bruce,

Thanks Bruce i understand that.

But can't i run free-surfer with all these parameters (size, spacing and orientation) ?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 8:22:38 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh

your best bet is to run everything normally, then convert the output to whatever format/orientation/voxel size you want

cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote:

...
   External Email - Use Caution
Thank you Bruse. Actually i converted the input into RAI orientation using mri_convert --out_orientation and gave RAI input the free-surfer through recon-all. The results are not generated.

My goal is to run free-surfer with RAI orientation and result should be in RAI. I also want the output of free-surfer with dimensions as 128*128*128 and spacing as 2,2,2 mm.

Can you tell whether this can be done using free-surfer?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Ritesh Mahajan" ritesh.mahajan@ripl.ricoh.com To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 1:44:40 PM Subject: run recon all with forced orientation, spacing and dimension

External Email - Use Caution

Hello Team,

As i know free-surfer generates the output with following:

Dimensions : 256*256*256

Spacing : 1, 1,1 mm

Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

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.

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

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

Ritesh Mahajan

12:22 p.m.

New subject: run recon all with forced orientation, spacing and dimension

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Thanks a lot Bruce for sharing this information.

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 9:50:44 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

cheers Bruce

On Thu, 10 May 2018, Ritesh Mahajan wrote:

...

   External Email - Use Caution
Hi Bruce,

Thanks Bruce i understand that.

But can't i run free-surfer with all these parameters (size, spacing and orientation) ?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 8:22:38 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh

your best bet is to run everything normally, then convert the output to whatever format/orientation/voxel size you want

cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote:

...
   External Email - Use Caution
Thank you Bruse. Actually i converted the input into RAI orientation using mri_convert --out_orientation and gave RAI input the free-surfer through recon-all. The results are not generated.

My goal is to run free-surfer with RAI orientation and result should be in RAI. I also want the output of free-surfer with dimensions as 128*128*128 and spacing as 2,2,2 mm.

Can you tell whether this can be done using free-surfer?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Ritesh Mahajan" ritesh.mahajan@ripl.ricoh.com To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 1:44:40 PM Subject: run recon all with forced orientation, spacing and dimension

External Email - Use Caution

Hello Team,

As i know free-surfer generates the output with following:

Dimensions : 256*256*256

Spacing : 1, 1,1 mm

Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

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.

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

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

Ritesh Mahajan

11 May 11 May

9:59 a.m.

New subject: run recon all with forced orientation, spacing and dimension

External Email - Use Caution

Hello Bruce,

1) I converted the my mri data from ALS to RAI orientation through command "mri_convert --out_orientation RAI inputALS.nii outputRAI.nii" 2) Then i gave a run for free-surfer, using recon-all command. After successful run of free-surfer without any error message, still i do not see any results generated by free-surfer. Any you please help why is it so ? 3) Under results mri folder i see only orig.mgz, orig_nu.mgz and rawavg.mgz. Other results are not generated.

Please can you explain why this happening ?

Thanks, Ritesh Mahajan

cheers Bruce

On Thu, 10 May 2018, Ritesh Mahajan wrote:

...

   External Email - Use Caution
Hi Bruce,

Thanks Bruce i understand that.

But can't i run free-surfer with all these parameters (size, spacing and orientation) ?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 8:22:38 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh

your best bet is to run everything normally, then convert the output to whatever format/orientation/voxel size you want

cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote:

...
   External Email - Use Caution
Thank you Bruse. Actually i converted the input into RAI orientation using mri_convert --out_orientation and gave RAI input the free-surfer through recon-all. The results are not generated.

My goal is to run free-surfer with RAI orientation and result should be in RAI. I also want the output of free-surfer with dimensions as 128*128*128 and spacing as 2,2,2 mm.

Can you tell whether this can be done using free-surfer?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Ritesh Mahajan" ritesh.mahajan@ripl.ricoh.com To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 1:44:40 PM Subject: run recon all with forced orientation, spacing and dimension

External Email - Use Caution

Hello Team,

As i know free-surfer generates the output with following:

Dimensions : 256*256*256

Spacing : 1, 1,1 mm

Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

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.

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

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

Bruce Fischl

2:55 p.m.

New subject: run recon all with forced orientation, spacing and dimension

Hi Ritesh

you need to give us much more information if we are to be able to help you. We need the exact command you ran, the full screen output of the command, and the contents of the subjects recon-all.log file in <subject>/scripts/recon-all.log

cheers Bruce On Fri, 11 May 2018, Ritesh Mahajan wrote:

...

   External Email - Use Caution
Hello Bruce,

I converted the my mri data from ALS to RAI orientation through command "mri_convert --out_orientation RAI inputALS.nii outputRAI.nii"

Then i gave a run for free-surfer, using recon-all command. After successful run of free-surfer without any error message, still i do not see any results generated by free-surfer. Any you please help why is it so ?

Under results mri folder i see only orig.mgz, orig_nu.mgz and rawavg.mgz. Other results are not generated.

Please can you explain why this happening ?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 9:50:44 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

because internally we expect things to be a certain way (which is why we convert the data to that format). There are also some requirements on the data that you have to meet. For example 2mm is not high enough resolution to get accurate cortical models. The acquired data has to be no bigger than about 1.5mm in any dimension.

cheers Bruce

On Thu, 10 May 2018, Ritesh Mahajan wrote:

...
   External Email - Use Caution
Hi Bruce,

Thanks Bruce i understand that.

But can't i run free-surfer with all these parameters (size, spacing and orientation) ?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 8:22:38 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh

your best bet is to run everything normally, then convert the output to whatever format/orientation/voxel size you want

cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote:

...
   External Email - Use Caution
Thank you Bruse. Actually i converted the input into RAI orientation using mri_convert --out_orientation and gave RAI input the free-surfer through recon-all. The results are not generated.

My goal is to run free-surfer with RAI orientation and result should be in RAI. I also want the output of free-surfer with dimensions as 128*128*128 and spacing as 2,2,2 mm.

Can you tell whether this can be done using free-surfer?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Ritesh Mahajan" ritesh.mahajan@ripl.ricoh.com To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 1:44:40 PM Subject: run recon all with forced orientation, spacing and dimension

External Email - Use Caution

Hello Team,

As i know free-surfer generates the output with following:

Dimensions : 256*256*256

Spacing : 1, 1,1 mm

Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

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.

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

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Bruce Fischl
Ritesh Mahajan