[Freesurfer] Is the slice delay of each slice needed for slice time correction with preprocess-sess?

[Maria Hakonen]

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Dear all,

Have I understood correctly that the slice delay of each slice is not
needed when performing slice time correction with preprocess-sess?

I am processing an open OASIS fMRI dataset. The dataset has fMRI data in
nifti format and JSON files that contain information about the data.
In the instructions they say: "Slice timing is included in the JSON when
available. Some original DICOM files did not have slice timing info. When
slice timing information is unavailable use the ratio TR/#slices."

The data is collected with a Siemens scanner.
If the slice timing is available it seems to be interleaved:

"SliceTiming": [
1.1025,
0,
1.165,
0.059998,
1.2251,
0.1225,
1.28750001,
0.1825,
1.3474,
0.245,
1.4099,
0.30499,
1.47,
0.36749,
1.5325,
0.42749,
1.595,
0.48999,
1.655,
0.55004,
1.7175,

Could I just run slice time correction with the siemens option?

Best regards,
Maria
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[Freesurfer] How to register fMRI data without upsampling voxel size?

[Maria Hakonen]

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Dear Freesurfer experts,

Could you please let me know how to normalize fMRI data without upsampling
the original voxel size from 5 x 5 x 7 mm to 2 x 2 x 2 mm? I have tried
this as follows:

1. Register functional (data.nii) to anatomical matrix



bbregister --s $subject --bold --init-fsl --mov data.nii --reg
register.dof6.dat



2. Register anatomical to mni152:

  mni152reg --s $subject



3. Create registration between functional and mni152

  mri_matrix_multiply -im register.dof6.dat -iim reg.mni152.2mm.dat -om
reg.mni152.dat



4. Resample func to mni152 space

 mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --mov
data.nii --reg reg.mni152.dat --o data.mni152.nii --no-resample



I checked the registrations after each step. After step 4, the functional
data and the template are not fully aligned if I use “no-resample”.
Without no-resample, the registration seems successful, but the fMRI data
has a voxel size of 2mm.

Best,

Maria
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[Freesurfer] register.dat file between fMRI runs?

[Maria Hakonen]

Dear Freesurfer experts,

I have used fslregister to register fMRI data to anatomical data.
However, now I would like to register all fMRI runs to the fMRI run that I
have registered to the anatomical data.

Could someone please let me know how to get a register.dat file between
fMRI runs?

Many thanks already in advance!

Best,
Maria
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[Freesurfer] Extract time courses corresponding to a brain structure from an stc file

[Maria Hakonen]

Dear Freesurfer experts,

I would like to extract time courses of certain brain structures from the
stc file in Matlab. Could someone please let me know how I can determine
the lables of 10242 verices of my stc file? Or is there some matlab
function that gives the time course of a barin structure.

Best,
Maria
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Re: [Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

[Maria Hakonen]

Many thanks for the answer!

Best,
Maria

2017-04-25 21:05 GMT+03:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>:

> -i{ijk}s will change the voxel size of the columns, rows, and slices,
> respectively
>
> -i{ijk}d will change the direction cosines of the cols, rows, slices
>
>
>
> On 4/25/17 11:47 AM, Maria Hakonen wrote:
>
> Dear Freesurfer experts,
>
> Could someone please let me know what is the meaning of the arguments
> -iid, -ijd, -ikd, -iis, -ijs, and -iks of mri_covert?
> From the internet and by typing mri_convert on the command line I only
> managed to find the following information:
>
> -iis, --in_i_size 
> -ijs, --in_j_size 
> -iks, --in_k_size 
> -iid, --in_i_direction   
> -ijd, --in_j_direction   
> -ikd, --in_k_direction   
>
> However, I don't still understand what is the effect of those argumnents
> in the following command:
>
> mri_convert gre_000.bfloat data.mgh -iid 1 0 0 -ijd 0 -1 0 -ikd 0 0 1 -iis
> 5 -ijs 5 -iks 5
>
> Are the arguments describing the direction and voxelsize of .bfloat?
>
> Best,
> Maria
>
>
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[Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

[Maria Hakonen]

Dear Freesurfer experts,

Could someone please let me know what is the meaning of the arguments -iid,
-ijd, -ikd, -iis, -ijs, and -iks of mri_covert?
>From the internet and by typing mri_convert on the command line I only
managed to find the following information:

-iis, --in_i_size 
-ijs, --in_j_size 
-iks, --in_k_size 
-iid, --in_i_direction   
-ijd, --in_j_direction   
-ikd, --in_k_direction   

However, I don't still understand what is the effect of those argumnents in
the following command:

mri_convert gre_000.bfloat data.mgh -iid 1 0 0 -ijd 0 -1 0 -ikd 0 0 1 -iis
5 -ijs 5 -iks 5

Are the arguments describing the direction and voxelsize of .bfloat?

Best,
Maria
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Re: [Freesurfer] dimension mismatch between source and mask

[Maria Hakonen]

Hi Bruce,


Thank you for the reply! I have now tried:


mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh
--tal --talres 2

mri_vol2vol --mov ribbon.mgz --reg register.dat --o ribbon-tal.mgh --tal
--talres 2

mri_convert -rl mri_data-tal.mgh ribbon-tal.mgz mask.mgz

mri_mask mri_data-tal.mgh mask.mgz masked_fmri.mgz

mri_convert masked_fmri.mgz masked_fmri.nii


I got:

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from masked_fmri.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to masked_fmri.nii...


However, when I opened the masked_fmri.nii in fslview, the masked_fmri
seems to be empty (intensity is zero and no brain is shown).

I would need to get a matrix containing voxels in the grey matter at all
time points. Could you please let me know what I am doing wrong above? Or
is there some better way to do this? I am new with Freesurfer, so sorry if
my questions are trivial.


Best,

Maria

2017-04-10 17:28 GMT+03:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:

> Hi Maria
>
> are they in register? If so you can do:
>
> mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz
> mri_mask fmri_data.mgh mask.mgz  masked_fmri.mgz
>
> cheers
> Bruce
>
>
>
> On Mon, 10 Apr 2017, Maria Hakonen wrote:
>
> Dear Freesurfer experts,
>> I have tried to mask fMRI data with grey matter mask as follows:
>> mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz
>>
>> However, I am getting an error " dimension mismatch between source and
>> mask".
>>
>> Could someone please let me know how to solve this problem?
>>
>> Best,
>> Maria
>>
>>
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[Freesurfer] dimension mismatch between source and mask

[Maria Hakonen]

Dear Freesurfer experts,

I have tried to mask fMRI data with grey matter mask as follows:
mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz

However, I am getting an error " dimension mismatch between source and
mask".

Could someone please let me know how to solve this problem?

Best,
Maria
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