Hi Douglas,

thank you for your time; I am trying to get the ribbon at functional space resolution (I need it to extract the white matter from my ROIs)

Here I am copying the 2 commands (one using .reg file, the second using .lta) I am using, and the terminal terminal outputs. Attached you will also find 3 screenshots from freeview with 1) original ribbon MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://owncloud.gwdg.de/index.php/s/fzFUAyWh5dbwyCb 2) ribbon transformed in functional space using the .reg file MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://owncloud.gwdg.de/index.php/s/0S0UJIoUdRk9IxK and 3) ribbon transformed using the .lta file MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://owncloud.gwdg.de/index.php/s/hvTEs3zRrRvskoX .

(Please Note: I am using Matlab to integrate this analysis in the general pipeline, so the command are started by the s=system() function )

%%%%%%REG

s=system(['mri_vol2vol --reg ' regpath ' --mov ' inputvol ' --targ ' funcTemp ' --o ' outputvol ]);

regio_read_register: loading lta

Matrix from regfile:

0.99982 -0.01069 -0.01533 -0.11505;

0.01423 -0.09676 0.99521 -0.84297;

0.01212 0.99525 0.09659 -5.72961;

0.00000 0.00000 0.00000 1.00000;

movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz

targvol FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii

outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz

regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta

invert 0

tal 0

talres 2

regheader 0

noresample 0

interp trilinear (1)

precision float (3)

Gdiag_no -1

Synth 0

SynthSeed 1649422337

Final tkRAS-to-tkRAS Matrix is:

0.99982 -0.01069 -0.01533 -0.11505;

0.01423 -0.09676 0.99521 -0.84297;

0.01212 0.99525 0.09659 -5.72961;

0.00000 0.00000 0.00000 1.00000;

Vox2Vox Matrix is:

2.01888 -0.03096 0.02351 23.93213;

0.02447 0.19504 -2.18955 197.85437;

-0.02873 -2.00955 -0.21287 240.49161;

0.00000 0.00000 0.00000 1.00000;

Resampling

Output registration matrix is identity

mri_vol2vol done

%%%%%%LTA

s=system(['mri_vol2vol --lta ' ltapath ' --mov ' inputvol ' --targ ' funcTemp ' --o ' outputvol ]);

Matrix from LTA:

0.99983 -0.01069 -0.01533 -0.11505;

0.01423 -0.09676 0.99521 -0.84293;

0.01212 0.99525 0.09659 -5.72960;

0.00000 0.00000 0.00000 1.00000;

Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii

INFO: src volume info differs from the one stored in lta. gets modified now.

volume geometry:

extent : (256, 256, 256)

voxel : ( 1.0000, 1.0000, 1.0000)

x_(ras) : (-1.0000, -0.0000, -0.0000)

y_(ras) : ( 0.0000, 0.0000, -1.0000)

z_(ras) : (-0.0000, 1.0000, 0.0000)

c_(ras) : ( 0.2540, 9.2232, 8.1562)

file : Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz

volume geometry:

extent : (104, 104, 69)

voxel : ( 2.0192, 2.0192, 2.2000)

x_(ras) : (-0.9995, -0.0137, 0.0296)

y_(ras) : ( 0.0126, -0.9991, -0.0397)

z_(ras) : ( 0.0301, -0.0393, 0.9988)

c_(ras) : ( 1.5530, 16.4346, 14.9788)

file : bold/template.nii.gz

INFO: dst volume info differs from the one stored in lta. gets modified now.

volume geometry:

extent : (104, 104, 69)

voxel : ( 2.0192, 2.0192, 2.2000)

x_(ras) : (-0.9995, -0.0137, 0.0296)

y_(ras) : ( 0.0126, -0.9991, -0.0397)

z_(ras) : ( 0.0301, -0.0393, 0.9988)

c_(ras) : ( 1.5530, 16.4345, 14.9788)

file : FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii

volume geometry:

extent : (256, 256, 256)

voxel : ( 1.0000, 1.0000, 1.0000)

x_(ras) : (-1.0000, -0.0000, -0.0000)

y_(ras) : ( 0.0000, 0.0000, -1.0000)

z_(ras) : (-0.0000, 1.0000, 0.0000)

c_(ras) : ( 0.2540, 9.2232, 8.1562)

file : Anatomy_Processed/hum_15496.long.long002/mri/orig.mgz

movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz

targvol FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii

outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz

regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta

invert 0

tal 0

talres 2

regheader 0

noresample 0

interp trilinear (1)

precision float (3)

Gdiag_no -1

Synth 0

SynthSeed 1649445621

Final tkRAS-to-tkRAS Matrix is:

0.99828 0.04446 -0.03809 2.43217;

0.03729 0.01869 0.99913 9.13850;

-0.04513 0.99884 -0.01700 12.13850;

0.00000 0.00000 0.00000 1.00000;

Vox2Vox Matrix is:

2.01577 -0.07692 -0.09781 28.12225;

-0.09113 -0.03433 -2.19744 198.19705;

-0.07530 -2.01747 0.04112 244.54424;

0.00000 0.00000 0.00000 1.00000;

Resampling

Output registration matrix is identity

mri_vol2vol done

Many thanks again,

Best

Giorgio

Message: 10

Date: Sun, 27 Mar 2022 17:16:25 -0400

From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>

Subject: Re: [Freesurfer] mri_vol2vol anatomical to functional

To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <50029d97-24be-17a3-2358-3c93982dea41@mgh.harvard.edu>

Content-Type: text/plain; charset=UTF-8; format=flowed

I'm not sure I understand what you are saying or what the problem is.

Can you provide the actual command line you are using, all the terminal

output, and a picture that shows what the problem is?

On 3/23/2022 2:46 PM, Manenti, Giorgio wrote:

> External Email - Use Caution

> Dear Freesurfer experts,

> I am getting problems to transform my xh.ribbon.mgh from anatomical 256x256x256 to functional 104x104x69 space.

> When converting the ribbon via ? mri_vol2vol ?reg REGfile ?mov INPUT ?targ funcTEMPLATE ?o OUTPUT ? and checking via freeview, i am getting the right functional space dimensions but the INPUT and OUTPUT .mgz are never overlapping. Why am i getting this misplacement ? Is this problem due to the register file i provide or maybe it is just a visualisation error (perhaps freeview is not the best way to check the conversion).

> I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) register.dof6.lta (changing ??reg with ?lta?). I am getting an almost perfect merge when using the .lta file but still the two volumes are misaligned.

> I tried mri_label2vol as well, but as expected i got worse results.

> To provide a minimum more detail, after recon-all i process the anatomy with the longitudinal recon. At that point i use the longitudinal anatomy to register the functional data, which i process by 1) mk-template 2) topup & applytopup.

> Many thanks in advance

> Warm regards

> Giorgio

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