Hi! Thx for your video! I have 3t functional data and I’m doubting whether I should do realign (est & reslice) or realign (est only). I have already unwarped with topup. As you can also reslice during coreg
Hi Maria. Can you tell me how to acquire the field map images in the labeled manner you have them here? I have a few different images that come off the scanner and only one of them actually says "phase". Any feedback on this is helpful. Thanks!
Hi, Thank you very much for the very helpful video. I was wondering how we can calculate the long and short echo times from filed map headers. I appreciate your kind reply.
Hi Maria! I'm a beginner on SPM12 and I would like to analyze some PET/CT data we have being producing at our University. Unfortunately I couldn't find good tutorials as yours on the internet. Do you think you could help me on this metter?
Thank you dear Maria Ironside for your comprehensive tutorial video about pre-processing fMRI data. When I watched this video and other videos related to the pre-processing fMRI data, I was confused about the volume information used in the segmentation step. In this video, the co-registered images are exploited as volume data whereas in some other videos the subject T1 image is used as volume data. Which approach is better or correct? My another question is about reorientation. Is it necessary for pre-processing the fMRI data? I really appreciate it if you could provide your answers for my questions.
Hi Alireza, In normalization we use the deformation fields from the segmentation step to move the functional data into standard space. Therefore, it makes sense to use the co-registered T1 to create these deformation fields, as it will be in the same space as the functional data and have the same starting point. In other uses of segmentation you would put the non-coregistered T1 into a segmentation module but for the purposes of preprocessing I think the co-registered one makes more sense.
Hi, does the slice timing parameters at 13:11 refers to the time each slice is scanned? I cannot find it on my dcm data. I have many .dcm files for a single subject. I checked several of them and none of them contains the slice timing parameters.
How to calculate EPI? What is the formula, where to look for the parameters ... I was looking for this answer in the video, and I did not find, alas, all the calculations in the video are already ready.
Hi, thanks for the videos! Very clear. At 32:45 you do the normalisation step and keep voxel size at [2 2 2]. I assume this matches your voxel size, but is it essential to change it to match the actual voxel size used in your study? I ran my steps with the default without considering it, but my actual voxel size is [3 3 3].
Thanks for a very useful series of SPM videos. Following these is however difficult because there are gaps in the audio. Is there any chance you have an intact version of the audio of this, so you can maybe overlap on top of this video? It'd be a shame for all this work to not be of use to those who found these video guides! Thanks again for your effort!
OK Thanks. Just one more question, I have a A->P phase encoding and an ascending slice order. I think my blip direction should be -1 right? I've tried to look at the field map toolbox but I'm not 100% sure still. Thanks!
Hi Maria, Thanks for sharing this valuable information. I am Asstt. Professor and my research scholar working in this area. I need few points to discuss. kindly provide your emailid. Thnks
![Fmriprep Tutorial [TRAIN-03-2022]](http://i.ytimg.com/vi/4W6qBIpE404/mqdefault.jpg)
that was the best instruction I ever found. I was struggling with multi-band for months and was lucky to see your video!
Just a note to say that I found this immensely useful. Just the right density of information for me.
I'm glad you found it useful!
Thank you so much, this has been the most helpful video I found on preprocessing steps!
Thank you so much for the excellent and detailed explanation! It is very helpful to me!
This has been extremely useful. Thank you so much!
I'm glad you found it useful!
Thanks for sharing this great tutorial! Fyi, VDM stands for "voxel displacement map" ;)
I'm glad you found it useful! Thanks for the reminder :)
Hi! Thx for your video! I have 3t functional data and I’m doubting whether I should do realign (est & reslice) or realign (est only). I have already unwarped with topup. As you can also reslice during coreg
Hi Maria. Can you tell me how to acquire the field map images in the labeled manner you have them here? I have a few different images that come off the scanner and only one of them actually says "phase". Any feedback on this is helpful. Thanks!
Hi, Thank you very much for the very helpful video. I was wondering how we can calculate the long and short echo times from filed map headers. I appreciate your kind reply.
Hi Maria! I'm a beginner on SPM12 and I would like to analyze some PET/CT data we have being producing at our University. Unfortunately I couldn't find good tutorials as yours on the internet. Do you think you could help me on this metter?
Hi, is it possible to find the dataset used in this video? I would love to follow along
32:12 you didn't edit that out :)
Thank you, wonderful tutorial!!!
Thank you dear Maria Ironside for your comprehensive tutorial video about pre-processing fMRI data.
When I watched this video and other videos related to the pre-processing fMRI data, I was confused about the volume information used in the segmentation step. In this video, the co-registered images are exploited as volume data whereas in some other videos the subject T1 image is used as volume data.
Which approach is better or correct?
My another question is about reorientation.
Is it necessary for pre-processing the fMRI data?
I really appreciate it if you could provide your answers for my questions.
Hi Alireza, In normalization we use the deformation fields from the segmentation step to move the functional data into standard space. Therefore, it makes sense to use the co-registered T1 to create these deformation fields, as it will be in the same space as the functional data and have the same starting point. In other uses of segmentation you would put the non-coregistered T1 into a segmentation module but for the purposes of preprocessing I think the co-registered one makes more sense.
Hi, does the slice timing parameters at 13:11 refers to the time each slice is scanned? I cannot find it on my dcm data. I have many .dcm files for a single subject. I checked several of them and none of them contains the slice timing parameters.
How to calculate EPI? What is the formula, where to look for the parameters ... I was looking for this answer in the video, and I did not find, alas, all the calculations in the video are already ready.
Dear Mam, I have T2w and resting state fmri data so is there a way to preprocessing them using SPM
Hi, thanks for the videos! Very clear. At 32:45 you do the normalisation step and keep voxel size at [2 2 2]. I assume this matches your voxel size, but is it essential to change it to match the actual voxel size used in your study? I ran my steps with the default without considering it, but my actual voxel size is [3 3 3].
Sorry for the late reply, yes, you should match your voxel size.
Hi I have some doubts in the video, how can I reach you?
Thanks for a very useful series of SPM videos. Following these is however difficult because there are gaps in the audio. Is there any chance you have an intact version of the audio of this, so you can maybe overlap on top of this video? It'd be a shame for all this work to not be of use to those who found these video guides! Thanks again for your effort!
Can anyone please tell that from where I can get fMRI dataset?
Why do you not apply VDM after calculating it? What is the difference?
That is done in the realign and unwarp step in this batch.
OK Thanks. Just one more question, I have a A->P phase encoding and an ascending slice order. I think my blip direction should be -1 right? I've tried to look at the field map toolbox but I'm not 100% sure still. Thanks!
@@ThePresident001 Sorry for the late reply, I'm sure you found out but yes, -1 is A-P
Hi Maria, Thanks for sharing this valuable information. I am Asstt. Professor and my research scholar working in this area. I need few points to discuss. kindly provide your emailid. Thnks