help > slice timing correction
Showing 1-5 of 5 posts
May 19, 2018 10:05 AM | jeonho lee
slice timing correction
Dear CONN-experts
I want to analyze the resting-state fMRI data obtained by using 3T Siemens Skyra scanner.
The parameters are the following: isovoxel of 2 mm3, TR=2 sec, multiband factor of 3.
After searching for the answer from the online webpages, some researchers recommend that slice timing correction is necessary in cases of TR=2 sec.
During slice time correction, I chose Manually define, and entered acquisition time of each slice(72 slice) obtained through the dcm2niix program.
However, in the preprocessing process, an error occurs repeatedly, and automatically returned as 1,2,3.......91.
Number of slices is... : 91
Time to Repeat (TR) is... : 2
Parameters are specified as... : slice indices
Completed : 11:46:44 - 22/12/2017
Done 'Slice Timing'
Running 'Slice Timing'
I can not understand what 91 means and why this phenomenon appears.
Any suggestion?
My question is very similar to what Larry did in 2017. I could not find the answer to that question and I was asked again.
Thanks for considering my request.
jh lee
I want to analyze the resting-state fMRI data obtained by using 3T Siemens Skyra scanner.
The parameters are the following: isovoxel of 2 mm3, TR=2 sec, multiband factor of 3.
After searching for the answer from the online webpages, some researchers recommend that slice timing correction is necessary in cases of TR=2 sec.
During slice time correction, I chose Manually define, and entered acquisition time of each slice(72 slice) obtained through the dcm2niix program.
However, in the preprocessing process, an error occurs repeatedly, and automatically returned as 1,2,3.......91.
Number of slices is... : 91
Time to Repeat (TR) is... : 2
Parameters are specified as... : slice indices
Completed : 11:46:44 - 22/12/2017
Done 'Slice Timing'
Running 'Slice Timing'
I can not understand what 91 means and why this phenomenon appears.
Any suggestion?
My question is very similar to what Larry did in 2017. I could not find the answer to that question and I was asked again.
Thanks for considering my request.
jh lee
May 19, 2018 05:05 PM | Larry Lai
RE: slice timing correction
Dear Lee
As of acquisition order, please choose Siemens (Interleaved). The CONN will detect it automatically.
• Even number of slices:
slice number 2 first
• Odd number of slices:
slice number 1 first
Example:
• 36 slices: even number of slices
• Order: 2,4,6,8,10,....,
34,36,1,3,5,7,10,....,33,35
• 35 slices: odd number of slices
• Order: 1,3,5,7,10,....,
33,35,2,4,6,8,10,....,32,34
For TR, please enter 2 in the basic setup.
However, you may always use MRIcro to check the total slice number by sliding the bar from the slice viewer on transverse plane.
Cheers
Larry
Originally posted by jeonho lee:
As of acquisition order, please choose Siemens (Interleaved). The CONN will detect it automatically.
• Even number of slices:
slice number 2 first
• Odd number of slices:
slice number 1 first
Example:
• 36 slices: even number of slices
• Order: 2,4,6,8,10,....,
34,36,1,3,5,7,10,....,33,35
• 35 slices: odd number of slices
• Order: 1,3,5,7,10,....,
33,35,2,4,6,8,10,....,32,34
For TR, please enter 2 in the basic setup.
However, you may always use MRIcro to check the total slice number by sliding the bar from the slice viewer on transverse plane.
Cheers
Larry
Originally posted by jeonho lee:
Dear CONN-experts
I want to analyze the resting-state fMRI data obtained by using 3T Siemens Skyra scanner.
The parameters are the following: isovoxel of 2 mm3, TR=2 sec, multiband factor of 3.
After searching for the answer from the online webpages, some researchers recommend that slice timing correction is necessary in cases of TR=2 sec.
During slice time correction, I chose Manually define, and entered acquisition time of each slice(72 slice) obtained through the dcm2niix program.
However, in the preprocessing process, an error occurs repeatedly, and automatically returned as 1,2,3.......91.
Number of slices is... : 91
Time to Repeat (TR) is... : 2
Parameters are specified as... : slice indices
Completed : 11:46:44 - 22/12/2017
Done 'Slice Timing'
Running 'Slice Timing'
I can not understand what 91 means and why this phenomenon appears.
Any suggestion?
My question is very similar to what Larry did in 2017. I could not find the answer to that question and I was asked again.
Thanks for considering my request.
jh lee
I want to analyze the resting-state fMRI data obtained by using 3T Siemens Skyra scanner.
The parameters are the following: isovoxel of 2 mm3, TR=2 sec, multiband factor of 3.
After searching for the answer from the online webpages, some researchers recommend that slice timing correction is necessary in cases of TR=2 sec.
During slice time correction, I chose Manually define, and entered acquisition time of each slice(72 slice) obtained through the dcm2niix program.
However, in the preprocessing process, an error occurs repeatedly, and automatically returned as 1,2,3.......91.
Number of slices is... : 91
Time to Repeat (TR) is... : 2
Parameters are specified as... : slice indices
Completed : 11:46:44 - 22/12/2017
Done 'Slice Timing'
Running 'Slice Timing'
I can not understand what 91 means and why this phenomenon appears.
Any suggestion?
My question is very similar to what Larry did in 2017. I could not find the answer to that question and I was asked again.
Thanks for considering my request.
jh lee
May 20, 2018 02:05 AM | jeonho lee
RE: slice timing correction
Thank you for your quick reply.
If I simply select "interleaved (Seimens)" instead of "Manually define" in the "select slice order" of the preprocessing step, then no further steps are needed for slice timing correction, Does it mean to be done automatically?
The version of the program I used is as follows. SPM 12, CONN v17
Thank you
jh lee
If I simply select "interleaved (Seimens)" instead of "Manually define" in the "select slice order" of the preprocessing step, then no further steps are needed for slice timing correction, Does it mean to be done automatically?
The version of the program I used is as follows. SPM 12, CONN v17
Thank you
jh lee
May 20, 2018 01:05 PM | Larry Lai
RE: slice timing correction
Dear John
Please see the attached screenshot.
The slice timing correction was included in the default preprocessing steps. In addition, you may want to add "functional Removal of initial scans (disregard initial functional scans)" to the existing preprocessing steps and please make sure you move it to top.
By the way, I found this site very helpful (http://www.nemotos.net/?tag=conn). Please use the Google translation.
Best wishes
Larry
Originally posted by jeonho lee:
Please see the attached screenshot.
The slice timing correction was included in the default preprocessing steps. In addition, you may want to add "functional Removal of initial scans (disregard initial functional scans)" to the existing preprocessing steps and please make sure you move it to top.
By the way, I found this site very helpful (http://www.nemotos.net/?tag=conn). Please use the Google translation.
Best wishes
Larry
Originally posted by jeonho lee:
Thank you for your quick reply.
If I simply select "interleaved (Seimens)" instead of "Manually define" in the "select slice order" of the preprocessing step, then no further steps are needed for slice timing correction, Does it mean to be done automatically?
The version of the program I used is as follows. SPM 12, CONN v17
Thank you
jh lee
If I simply select "interleaved (Seimens)" instead of "Manually define" in the "select slice order" of the preprocessing step, then no further steps are needed for slice timing correction, Does it mean to be done automatically?
The version of the program I used is as follows. SPM 12, CONN v17
Thank you
jh lee
May 24, 2018 10:05 AM | Alfonso Nieto-Castanon - Boston University
RE: slice timing correction
Dear Lee,
Two quick additional comments about this case:
1) my guess is that perhaps you are seeing 91 slices (instead of your expected 72 slices) because you may have normalized your data prior to slice-timing-correction (normalization will resample your data by default to a canonical voxel-size and bounding-box). This is not the recommended approach, and slice-timing correction is typically recommended either as the first step of preprocessing or as the second step (right after realignment). See for example the default preprocessing pipeline in CONN for reference. If you are already using the default preprocessing pipeline, this probably means that you are trying to re-apply the preprocessing pipeline to an already-preprocessed dataset (already in MNI-space), so simply go back to your original data in the CONN gui 'functional' and 'structural' tabs before re-starting your preprocessing pipeline and that should fix this issue
2) when using multiband sequences (e.g. MB=3 in your case) you need to specify slice-times instead of slice-order for slice-timing-correction (i.e. enter a vector with 72 numbers specifying the acquisition time in milliseconds for each slice). For example, in your case this may look something like the following sequence: 0.0 83.3 166.7 250.0 333.3 416.7 500.0 583.3 666.7 750.0 833.3 916.7 1000.0 1083.3 1166.7 1250.0 1333.3 1416.7 1500.0 1583.3 1666.7 1750.0 1833.3 1916.7 0.0 83.3 166.7 250.0 333.3 416.7 500.0 583.3 666.7 750.0 833.3 916.7 1000.0 1083.3 1166.7 1250.0 1333.3 1416.7 1500.0 1583.3 1666.7 1750.0 1833.3 1916.7 0.0 83.3 166.7 250.0 333.3 416.7 500.0 583.3 666.7 750.0 833.3 916.7 1000.0 1083.3 1166.7 1250.0 1333.3 1416.7 1500.0 1583.3 1666.7 1750.0 1833.3 1916.7 NOTE: this is just an example, it assumes ascending order of slices with MB=3, but check with your physicist to figure out the actual order of your multiband sequence (e.g. it may be interleaved ascending instead of simply ascending). I believe from your description that you are already doing this correctly but I just wanted to double-check
Hope this helps
Alfonso
Originally posted by jeonho lee:
Two quick additional comments about this case:
1) my guess is that perhaps you are seeing 91 slices (instead of your expected 72 slices) because you may have normalized your data prior to slice-timing-correction (normalization will resample your data by default to a canonical voxel-size and bounding-box). This is not the recommended approach, and slice-timing correction is typically recommended either as the first step of preprocessing or as the second step (right after realignment). See for example the default preprocessing pipeline in CONN for reference. If you are already using the default preprocessing pipeline, this probably means that you are trying to re-apply the preprocessing pipeline to an already-preprocessed dataset (already in MNI-space), so simply go back to your original data in the CONN gui 'functional' and 'structural' tabs before re-starting your preprocessing pipeline and that should fix this issue
2) when using multiband sequences (e.g. MB=3 in your case) you need to specify slice-times instead of slice-order for slice-timing-correction (i.e. enter a vector with 72 numbers specifying the acquisition time in milliseconds for each slice). For example, in your case this may look something like the following sequence: 0.0 83.3 166.7 250.0 333.3 416.7 500.0 583.3 666.7 750.0 833.3 916.7 1000.0 1083.3 1166.7 1250.0 1333.3 1416.7 1500.0 1583.3 1666.7 1750.0 1833.3 1916.7 0.0 83.3 166.7 250.0 333.3 416.7 500.0 583.3 666.7 750.0 833.3 916.7 1000.0 1083.3 1166.7 1250.0 1333.3 1416.7 1500.0 1583.3 1666.7 1750.0 1833.3 1916.7 0.0 83.3 166.7 250.0 333.3 416.7 500.0 583.3 666.7 750.0 833.3 916.7 1000.0 1083.3 1166.7 1250.0 1333.3 1416.7 1500.0 1583.3 1666.7 1750.0 1833.3 1916.7 NOTE: this is just an example, it assumes ascending order of slices with MB=3, but check with your physicist to figure out the actual order of your multiband sequence (e.g. it may be interleaved ascending instead of simply ascending). I believe from your description that you are already doing this correctly but I just wanted to double-check
Hope this helps
Alfonso
Originally posted by jeonho lee:
Dear CONN-experts
I want to analyze the resting-state fMRI data obtained by using 3T Siemens Skyra scanner.
The parameters are the following: isovoxel of 2 mm3, TR=2 sec, multiband factor of 3.
After searching for the answer from the online webpages, some researchers recommend that slice timing correction is necessary in cases of TR=2 sec.
During slice time correction, I chose Manually define, and entered acquisition time of each slice(72 slice) obtained through the dcm2niix program.
However, in the preprocessing process, an error occurs repeatedly, and automatically returned as 1,2,3.......91.
Number of slices is... : 91
Time to Repeat (TR) is... : 2
Parameters are specified as... : slice indices
Completed : 11:46:44 - 22/12/2017
Done 'Slice Timing'
Running 'Slice Timing'
I can not understand what 91 means and why this phenomenon appears.
Any suggestion?
My question is very similar to what Larry did in 2017. I could not find the answer to that question and I was asked again.
Thanks for considering my request.
jh lee
I want to analyze the resting-state fMRI data obtained by using 3T Siemens Skyra scanner.
The parameters are the following: isovoxel of 2 mm3, TR=2 sec, multiband factor of 3.
After searching for the answer from the online webpages, some researchers recommend that slice timing correction is necessary in cases of TR=2 sec.
During slice time correction, I chose Manually define, and entered acquisition time of each slice(72 slice) obtained through the dcm2niix program.
However, in the preprocessing process, an error occurs repeatedly, and automatically returned as 1,2,3.......91.
Number of slices is... : 91
Time to Repeat (TR) is... : 2
Parameters are specified as... : slice indices
Completed : 11:46:44 - 22/12/2017
Done 'Slice Timing'
Running 'Slice Timing'
I can not understand what 91 means and why this phenomenon appears.
Any suggestion?
My question is very similar to what Larry did in 2017. I could not find the answer to that question and I was asked again.
Thanks for considering my request.
jh lee