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

[Douglas N. Greve]

Yes, you can use the siemens STC option (ie, -stc siemens)

On 2/26/2024 9:02 PM, Maria Hakonen wrote:


External Email - Use Caution

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

[Maria Hakonen]

External Email - Use Caution

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
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.