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and for the full processing procedure actually you can see there are so many different steps right here and actually this is a pretty complicated but if you want to do it in a simple way in a simple way actually again you can use the you can use so called the page process right here I mean this one that actually you can see that we will in a very first step we will do the correction for slice timing I will actually explain well why we need to do these kind of steps behind all the process but in this very first slider I'd like to show you the whole procedure record and then the second step we will do the realignment because during the during the imaging you cannot guarantee that the subject really fixes or cubist in did a movies and it's pretty hard to say so so actually we will check whether the head has any motion during the whole scanning time and if there is significant motion we will do the realignment till actually use for example the very first slide or we can use the imaging fallen that acquiring in the middle of the skin and let all other images realign to this specific one to ensure that actually imaging from different time point has the same spatial information okay and the third step would be the co-registration as you may record that we have to at least the two data set one is so called fmi epi data set with low spatial resolution but with the both information we see another one is a high resolution anatomical imaging now we'd like to call register the high resolution anatomical imaging to the EPI images so we can not only have the function information but also have the corresponding structure information mrs. s table are going to do and for the first forces taper we are going to do dinner validation this is so called spatial normalization that we'd like to get rid of the variation from subjects headship or head size we would like to actually unify the hand shape or head follow so this one tote so called spatial normalization is trying to normalize your head shape and antenna size weighs a standard heavy images this is the space as specific step that we are going to do and this most establish is actually again the spatial smoothing with the light tail make the imaging looks like most most nano means a little bit blur but it actually can help us to reduce the noise that contender in the images this is so called spatial smoothing and a final finally we will perform the image segmentation segmentation means that we we are going to classify or identify different tissue therapy we see the brain regions we will focus on specific three different things Korea metric my mentor and CSF so called cerebral spinal fluid regions right with each of the step actually SPM will generate or create so many different files well to differentiate all the files generated from different steps actually SPM well gave specific prefix of the fountain right for example if you perform the slice timing all the generated file from this step well has a prefix with a small a right B so if you see the fountain start with a actually this is the products from sliced timing correction if you see the fountain can start with an R right here you can see actually this is the production from the so you can see actually the prefix well accumulated right here you can see the first step is a right so you can see the file name is a right here then followed by the realignment then you can see our right here the a normalization will give you a new preface like W so actually you can read the prefix to see what kind of the previous step actually performed or applied to this in Genesis so you can see for this one actually I can know the first step is actually the spiced timing a or realignment W normalization yes actually for the suite just motion so this is the way how this system worked to differentiate the different steps right and after they find out one actually second region will generate several different files actually started with it mostly right here see one represent the gravity say 200 meter see three CSF right view and you can see they may have a different files that for example this one this is actually the essential one actually the six color parameters to represent the whole head motion three translation three axes the translation and the three rotation angle right there it will all recorded is in one text fat regime okay well this kind of the funds will be used in later presented but this line is again a lookup slider or lookup table for you that if you really want to know why I have this file we sing my general folder we can just check out which kind of step actually generate these kind of files okay before I explained each step in detail I need you to start let your computer busy processing so we won't waste the time so what do you should do right now is go back to SPN menu figure right here and now please click batch button right here there is a page button right here again you will see a very actually these in pharma is called a editor manager means that I can do so many different things in a sequential order and we can do other things step-by-step so instead of that click everything of button manually you can actually put all the functions all the modules in this page once you set up all the parameters you should click one button right here then all you need to do is wait okay so now we are going to actually perform so many different steps right here you don't really need to setup by yourself I already set up a batch file for you so what you should do is now click the load the page button right here now there is a badge underlined fmi pre-process the main file right here this is the setup for this batch process and now you can see there are so many different steps that that all I already set up for you and I'm not going to explain right now I am I am to let you start working right now so what you should do is actually you can just actually enlarge this figure little bit so actually we can see a sign of these steps right here actually there are some information right here for each step normally you need to specify the first that letter will be processed in this specific state however you can see that actually only three steps three states a specific state this one this one in this one actually it amends the input as I mentioned that if you see the left arrow with uppercase X right here that means you need to specify the Fabri here and for the others actually can only see the DEP this actually represent the dependency that means I don't really need to specify the import Ferris right here because it will automatically depend on what you specified in the previous step so this is clever design I actually don't really need to Samantha all the files right here you don't depend on the previous one you know what depend on just some files before they step so you can see you only need to specify the three phasma here okay but before we actually specify the file we actually need to adjust the song setup right here so in the next slide you can see the very first one we need to get adjusted is actually for this step what we need to adjust that this fountain right here because the file paste the file path is actually different between computers this one is actually for my desktop to PC not of yours so before you can do anything I asked you to actually modify this page file so it made the file path on your even notebook or your desktop PC so please go to this step and right here just click on least one normalize normalize estimate this one as you click this step you can see actually there is one specific save a file called tissue probability map right here then you can see this path is definitely not your past it's my past so what you need to do is actually to modify this file so you can do it again just double click now you will see again the final selection figure right here okay however there is already one file be selected right here right so what you should do is actually unselected these how to do so just click click the file left-click your mouse then you can all select this or again you can right click your mouse and the select the unselected oh is the same thing so now you are able to select a new file right here so where this tissue tissue probability map is located actually this file is located that we see the SPN child folder if you remember the past when you actually for example to me I actually download the SP and health to these specific pests you need to come to this SP Intel folder right here then go find a subfolder named TPM okay then you will find that there is a specific file called TP and that my this is the specific value NICU selected okay please remember it is a store the SPN childhood folder just find subfolder TPM that you will find this file now you can just click for one time just one click this file and press done and now it will update it to the right correct file parents for your computer these are the very first things you need to do okay and next day they are two steps of you need to again update the file plans for TPM ok I promise you if you didn't change the computer for the imaging process you only need to do this for once ok so don't worry about this step okay so come to this segment second - step right here they are you can see 1 2 3 4 5 6 6 Malpass you need to modify actually so let's do it one by one it takes time but it's essential stability you need to do so again double click now I'm select this one again I can go back to the the folder that I selected what you can do is actually you just find the previous one here is a selection it will automatically at least the folder that the you previous previously selected so it's very convenient just go to the previous option and just pick the final one this is a final one that you just pick this one okay and right here there is a very important things you need to do is actually we see this teepee and my file is it actually content six-six maps for a different issue in greek rhythm grandma trio by major CSS and also ska scalp and i think the background teacher or something actually there are six different maps we see in this file then that's why actually there are six is six a file you need to specify so what you should what you should do is actually you need to input these you need to give this information so SPN can know that actually there are six six map content within this file please key in correctly okay then you press enter right here or you can use this kind of affect your form right here one with a space to with a space three four five and six then it will actually expand expand them this file into six different method you need to specify there are actually six maps that we see in this part right here and now what I can do for this very first one you can only select the one right here first one press down the older majors the older is very important because the very first one represent represent the grand major map okay the second one is actually the five meter map so what I can do right here again I can show you go to this one expand the BT p.m. found right here select now select the second one okay and then come to the third one again come to the right folder phrase this one okay third one okay I'm not going to explain anymore so I'm going to just go through all the all the files please do it by yourself so every single time you switch the computer to do the analysis you need to do this step because the file face is definitely different okay now I picked a fixed one final one is the six one okay I'm sorry six one thank you okay so this is the corrective file path but again we have to segment I will explain to why we have to second mistake right here but another one please do the exactly the same thing just modify the pass okay first one second one sir two one okay certain one Force one it's really a tedious process with you you just need to do this for once so please be patient force one save someone and then the final one this one six one okay now I have to modify to all the pathways here once the modification is done please please do sieve this bench before you do anything else because you don't really want to go through all the modification again and over again every single time when you open this page editor you don't want to do so so now please please just save this modify the page file you can actually overwrite just overwrite because you don't need to just you don't need to keep the original one because this has the wrong file path right just overwrite it so yes just overwrite it so this is a very first thing you need to do and once this is done you never need to do this step anymore if you if you don't change the processing computer document and then what we should do right now is now we can really specify the imported over here and what's the first one actually we will select the directory that means the SPN well automatically switch the current folder for you so you can have all the output or already created a dataset in the correct folder so you need to do so okay so this start from the first one pick the right folder so I'm going to select the right folder right here actually we see in the process again I don't like to mix the process data with the raw data say right here so I will select the process and one thing okay now let's do this one so I click the one part right here means the current folder I'm sorry do it again right here so now it's actually located the process the one Baker telephone thank you and then come to the slice timing it's nice timing right you need to specify the station station means the whole fallen State for the every marketer no just topically now I can go to the processed one back and you can see it's actually only select Oh only a hundred and sixty-five five pass right here nothing else because we didn't start the process a hundred sixty five cities is the right final numbers for the one back okay and then for the thirteenth of it right here this one is actually performed the image co-registration so we'd like to call register the structural imaging to the functional imaging the EPI interview so you can see the reference imaging is actually the real line or resizing is actually the process the EPI interaction but now what we are going to do is to specify the source image right here colleague now what I'm going to do is to select actually the MP reg right here you can actually directly select the MP range and the selected file right here however I don't like to do so I actually will copy I will copy the MP range folder into the one peg file actually I will do so why because normally we're seeing one mm I study we may have multiple station for different functional tests for example we have actually won back-to-back picture naming and the multitask actually so each one we will perform the imaging co-registration I don't want all the imaging correlation we saw well mix that we seen this one folder if we have one big folder to pack folder I'd like to have one specified structural imaging for one's functionalisation so actually I will copy the MP relative into the one functional folder right here for example one pack folder right here so I'm not going to process this one I will actually process the file we see the white backpack so if I have another folder for for example to back for example to pick right here actually I don't well again copy these mph into this stuff will do okay so just I don't want to mix all of it is kind of my happy to do so so now in this situation actually I won't pick this one I'll go to one pack select EMP rage I will use this this one the structural image right click OK once everything is selected you may see that actually the again the rampage pattern is now functional so you can actually press the bottom I'm going to introduce each step to you but now if your finishes that are please just press the wrong page button right here when you should be able to see again the processing part is now currently process something and you can go back to the America command window right here is actually displaying what is the current step right now so now it is is doing this nice timing correction right now and now I can see this nice timing process is done now it's go to the realignment step right here so all the process will be other steps where we process the step and step depends on the module least module a strike you okay so we can just wait in my tanks I think depends on you are your PC performance it may cost the 5 to 10 minutes for one case actually so now we should go back to the slide so I'd like to explain the each step but why they need to perform this kind of the processing step for the very first one is the correction for slice timing actually although we claimed that we actually has the temporary solution around 2 seconds that means we can repeatedly acquire the whole brain imaging we sell time interval to second but actually even in the same time point for example the very first standpoint the different slice that are acquired during these specific time points actually different for example in mi system actually we may take a couple minutes ekend for a quiet one cycle imaging so for the example this one may acquire in the for example the European second but this one images lines may actually acquire in the five millisecond then come to the ten minute second fifteen minute second and twenty milliseconds there is actually a very slight slightly different slice timing actually the image timing between slices right there and this kind of the difference temporal difference actually met costly misunderstanding of the bowler signal profile right here as you can see this is actually the major the polishing know if you plan that actually we acquired every single slice for this example five slices in a same time point you may look the polishing law in this way the postman looks like in this way however if you correct correct the slice timing difference right here you can see actually we are not quite in the same time point there are slight difference right here so the horizontal axes represent the timing as you can see actually these slices are quite easy in this time point then this time point this time for this time point is double if you really want to claim that they all acquiring a center point you need to correct at the timing so now if you try to correct a time point from this one to this one or this one to this one what you need to do is the interpolation you need to interpolate the value from based on this one to this one or between this one you can have this one is the integer ten point right here so this is the actual actual polishing Kanaan you should have hell not this one because you actually ignore the sliced time difference for different images slice right here so though the time is actually really really small it's in the millisecond level but actually it may change the Baltic profile right here so this is a very first step you need to do for the LMI data ratio and the second step is actually to correct a hand motion actually right here this is actually the innominate in image right here you can see actually there is some kind of position or with the hand movement when you try to display all the fmi from the one single slice in this image you can see actually the brain is actually moving but however in a very very small way however you can actually quantify the hand motion using the realignment technique over here so you can see the result right here actually we can see three translation translation means that the head movement allows for a specific axis for example X represent left and right one represent front and behind and the anterior and posterior and Z represent the head in the same direction so you can see actually you can find out across different time point right here for example this galaxy has 240 different follows or different time points right here you can see this axis translation is actually pretty obvious right here although the translations actually in I think below 1 millimeter is actually pretty small but - it does exist right here and not only the translation you can also major the rotation so we have three different rotation angle maybe I can show this light right here not only 3-axis translation we can actually see peach it's more like nothing your head and euro and the yoke just like three different three different the rotation angle right here so actually you can again try to quantify the rotation value across different time points right here so you can see actually the degree again is very small actually under maybe point six five years there's some stressful that we normally use to for for the criteria whether we should exclude the data if the subject actually had a head motion larger than three millimeter and the rotation again larger than straight degree then normally we will exclude the data because that means the subject actually had very significant emotion also you can actually correct the emotion however this kind of the head on Oakland the movement actually insert a very very huge variation or signal change for your post signals so even you can correct we had a motion the profile for posting remains still affected in a very very huge way so actually if we after the estimation of the head motion we can see the speaker and in return I will check the value if larger than three meters and the laundry and three degree we were just excluded data that means the participant actually didn't call collaborator pretty well even just to comply with your order that keep your head fixed and to not moving ahead actually he is moving his head or something so this is a very important step that we should confirm the data quality and then the co-registration actually we will call register the structural t1-weighted image into the API so you can see this one is actually the FMR you get image right here you can see the Academy spatial resolution is actually pretty bad right here however for the structural team imaging you can clearly define the powder of the agreement and the five major the spatial resolution is high so what we are going to do is actually we try to make these two images do not say we see in the same position what we see in the same location to do so you can use so-called the imaging coloration technique actually in SPM may use the rigid Body Transformation rigid body means that you won't actually change or modify the internal structure of your print you're actually only rotate or just lane to your imaging this is called rich body why we do so because is this two different images they are actually originating from the same subject so you don't anticipate there is any the transformation of the imaging that actually will change the shape or something it's only allowed the rotation of translation and in ESPN they use the bridge management of transformation waist the mutual information is the cost function so we can automatically finish or achieve the very good image college situation so you can see this is a result that will try to plot the boundary of the EPI data on the structural image right here actually you can see they mentioned pretty well you can see the powder of the brain tissue or the powder of the practical ventricular area is actually aligned pretty well so in SPN you can either using the automatic process or it actually give you a chance to actually to do the menu image composition however it takes time actually and it definitely will ensure some operator variation meaning of this kind of image so normally we will use the automatic processes that are using major information to tell the rigid body transformation to ensure that the structural image is actually a light or courage call registered to the API data so now we not only have the functional information but also we can have the clear definition of the cortex location or critical location and the next thing that would be the specialization as I mentioned that actually different participants may have different brain fallen or apprenticeship however if we would like to perform some group of wise group wise means we would like to pour different subjects data together that means we need to unify the spatial spatial geometry or spatial information or spatial coordinates whatever so what we can do is actually there to way actually you can use the code registered anatomical or structural imaging to do the specialization actually in this way you can have a better result because these spatial information is actually pretty good in anatomical imaging however in SPM you have another option you can actually perform the normalization solely use the EPI data you can do so because we also have a so called epi template right here so you can actually normalize the subject API directly to the EPI template you can then still have the so-called normalize that you getting them however this this approach may have a poor result because the spatial information contained in epi is actually a little poor compared to the anatomical to language so the normal procedure or the procedure that I actually give to you the story the page that I said it's actually used this way we will first use the subject anatomical imaging to do the spatial transformation what is the reference image is actually the t1 template as you can see this t1 template imaging is actually acquired I think they are quite a base of a hundred and fifty fifty two different subjects they'll try to realign these 150 different subjects head imaging after the alignment that you try to do the imaging average so you can see this image is a kind of the blurred it's over smoothing I can say however this is actually acquired from population so it may be a patriot representation of the average average brain geometry right there so what we are going to tell you is we try to estimate how can we transform these imaging to this so-called template images but in this kind of the spatial normalization we no longer use rigid body transformation as I mentioned that rigid body transformation didn't allow any significant change of the brain it's only allow you to rotate or translate your brain but not allow you to change the ship however in this step we anticipate you unify the branch geometry so we need to allow so-called nonlinear nonlinear transformation or non mania imaging transformation so we not allow the algorithm to really modify or change the apprenticeship or brain geometry right now okay and then after this kind of translation now you can have so-called normalize the t1 right here so this is the original or the native t1 right here and this Y is actually the normal esta t1 so you can see original tu is actually a little how to say these are short in the things compared to the T one template right here here is longer than this one however after the utilization you can see the axes are growing more like to the template right here so actually if you have ten subjects on him you will feel this kind of specialization to ensure all the subjects they have a very similar spatial geometry however will only modify the spatial geometry we didn't change we didn't change the profile of the total signal okay after these kind of the estimation of transformation we now can apply the so-called transformation matrix these transformation matrix actually records how we how we transform one specific coordinates or the specific spatial geometry to another one in this example is a highway transfer they subject the geometry to the normalize the geometry so now we can directly apply this kind of a transformation to the EPI data remember that we already purchased registered with t1 images to API so we can apply the same transformation matrix directory to the subject API so we can have the normalized API right here this is the preferred the process for at least for me or I think for most of the researcher that we didn't like to perform the specialization through the anatomical imaging and they apply to the API and then we will perform the so-called special supposing as you can see right here this is the normalized image right here after the specialization you can see now the friend geometry is more like a unified one it's just like just a pretty one to me actually - we will perform the spatial mostly right here special supposing means that we will apply the 3d koushin kernel if you know the convolution if you know the kernel you may understand what I'm talking about if not you may go to well my class and well my course called Mara but you can try to figure out how we can perform the images in this case actually after the image is smooth you can say this is the product this is the result you can see the image you become more polar compared to the original one also we may lose the spatial information however we have another anatomical image on hand we don't really worry about the spatial information in this image we actually want to reduce the noise in the village right here so what we are going to do is Emily smoothing well actually average or we called weighted average not only ways by the original pixel but also we will consider the surrounding paths so we consider the ferry from the surrounding voxel and perform these so-called weighted average so we can generate a new result however once we try to do this kind of process we try to or we will make the neighboring pixel have the stimulant value compared to the original one and that's why this nice Muslim imaging looks like a more pure water here however this kind of a process can help us to reduce the knowledge because the original assumption that no it's more like the old white noise that means it well went only this repealed in the entire image if you do the spatial average or smoothing it can temporarily wipe out or average out all the noise come component within the energy so this approach will help us to actually increase the signal-to-noise ratio and also help us to have a strong more strong statistical power after we try to do some static statistical inference writing there is one thing that you should keep in mind this step image is supposing it's not always necessary for all the analysis in particular analysis such as the multivariate the Pentagon sees this step is forbidden you cannot do this step because this will practice something the MVPA so remember sometimes we need to remove the smoothing from our page process because this is not necessary for some kind of things but for the brain activation analysis and for the brain cognitive analysis I think this step is essential you can use this to improve the signal to noise ratio and the final step is the teacher certification as I say that after the teachers condition we actually will be able to identify which imaging region is the cremator which region is one meter and which is CSF cerebral spinal fluid region you can see this is a result once you finish the images accommodation step you will have at least a three different file start with C 1 C 2 and C 3 right here C 1 for cremator sitting for my major in the state 3 for CSM if you just view the file in the a micro you can see actually you will have put you a white region for the parameter actually the values within this region is around 0.8 to 1.0 that means you have very high probability to clear that this area belongs to gravity again for 1 meter you will have very high ferry between 0.8 to 1.0 to claim that this white or bright region belongs to 1 meter again policy yourself so this is actually the so called tissue map or a teacher probability map that we use to identify which is the parameter specifically this one so we can study the brain function specific on the chromatin region normally we don't we are not interested in Miami the region or CSF region for brain function in the whole study ok no we focused on the parameter which okay so right now I believe my Melba has finished all the process right here so you can see there is completed completed and the tongue makes it right here that means you just finish all the process right here so now you can go back to the folder right here now we can see this is the original image right here okay and then I mentioned that actually for the very first step the slice timing you will have the new files that has a prefix of is a right here so again now go into your folder you can see okay now plenty files start with just the the lowercase a right here again the number should be a hundred and sixty-five right here let me comfort thank you you have a hundred and sixty-five files right here that means each or regional file will have these sliced timing process ranking high in France nice timing didn't change at any special geometry so I think it's very hard to stay to see or what you tell what's the difference between the original one and the direction force nice timing files writing and then that we are realignment you can see that should start with the are let me check this one stone weights are right here you can see the second word is a that means this already has this nice timing correction then come to the right here and then the next tape should be the low noise right here you can just click it up you right here now your Devon can tell the difference right here so I'm going to open the new a micro right here this one okay so now we can compare on your left hand side this is the normalized imaging on your right hand side this is actually the original image the image geometry is pretty different this is the original one so you can see this is more like the software or regional headship but this one is normalized to the extender t1 template so you can see actually this is more more standard geometry right here the symmetry the size is better okay and then the final one is the smoothing data we'll start we sit and ass right here so now we can again show the s5s right here so many far has yes maybe I just try to find by myself this one star waste ass right here so I can see this is the supposing to stay right here compared to only normalize only in the utilization but who knows images smoothing right here so this is the smoothing Tennessee actually for the subsequent analysis we will use this this final one this most intercepts for the analysis not this one we will use this one and the for the segmentation step but you can see that we may have c1 c2 and c3 file right here these will actually stay except in the subfolder of the structure image and peer edge right here so you can see you actually we have so many different c1 c2 c3 and also c4 in a c5 you can just check c1 it's for perimeter region C 2 for 1 meter region C 3 for CS f c4 actually for I think for Scott discovery you right here and C fine for skelter analyzing some surrounding from the teacher writing so the very first one c1 is the one we are going to focus down on the print function is this one okay so with this process and with all the files you may say that okay we finish the imaging processing but there's one more step I'd like to reminding you is this one I recommend you to always check your data how to check when you use this kind of the page processing it's actually pretty hard to see each step because everything will sequentially automatically processed so what you can do is actually SPN well generate some kind of local file that means the record of the process it was started with the SPM so now you can search for a file start with ESPN this one is actually an PS file PostScript file if you want you see this you definitely need to convert these to the PDF file so we can read this so I give you an link actually this is online online comforter for free use so actually you can you can go to this website and the one you can do is upload it just upload this file please click file to the and process the Surrey process in a one pack okay so now you can see SPN this one okay you will see there is a specific date that the thing you process the data is well these days they found out okay then just press comfort comfort to PDF a so you can just check the process stairs just wait a couple seconds okay so now this is the PD and found that they need comfort for you so just open this and now you can see this this is the log file that for example how the subject how our participant cooperated with cells so easy the translations actually pretty small because this is only in SAP a mini meter playful so I think our participant did a very good job and translation as you can see is around point one two minus point four degree right here yes still good enough and then this these is actually help you to see whether the Conservation Corps registration doing good on that so you can see this actually the the corresponding cause ever here so we can see the imaging controversy so I think yeah at least you can check this essential part the ahead emotion this is a very important one it's the head motion is too large I definitely will recommend you to excellent in acid or reacquire that it has it from the participant okay so I think that's all the steps that no way we can use SPM to do so however if you look very carefully into the page file you may find out there are so many different parameters that I may spend some time the next week tell you why we or how is it over this kind of parameter okay so I think that's all for today is the enclosure