Welcome to my page

The blog contains different interests of mine (referred to in the tabs ). Feel free to browse them and make any comments/ suggestions you would like to make. Hope you like the blog. Enjoy..

Computer fantasies

Computer Fantasies: This page contains computer related stuff - tricks, tips, hacks, cool stuff that i have learnt from different places. hope you like it.

Know my research

Know My Research: This page contains my research ideas and comments.

Literary interests

Literary: This page contains my literary interests.

Hard days

As other posts, this one comes far too late.. after years. That could just mean one thing and one thing only - I am really sad. The worst thing is that there isn't a thing that is wrong. Everything is working, my work is fine, I have friends who care. I have family that loves. But I am just sad.. sad for myself and the things around me. Something from the inside is not right.

I am still chasing things in the air, things that don't really exist anymore. Things that I ended. Things that I regret ending. Things that churn my guts from the inside, twist me and choke me down. After 2 years u would have guessed it would have passed, but who knew a bit of liquid push is all it needed to get to the bottom of my sorrow. who knew it could be so deep, who knew that it still existed down there.

I hope to come out of this and for that I leave it forever.

Moving on...

Humans like to stick to things the way they are and probably I am no exception. Perhaps there  are people who like to try new things but even those people always content that there is something stationary in their life that they can hold on to. I think we all want to be secure about something in life; things that are concrete and will hold no matter what. Unfortunately, for people like me that’s just about everything – a pen, a house, an office or a relationship. I end up thinking it will be forever. I end up thinking that things will hold even if they are destined to end. We just have to learn how to move on with life. 

We have been in this office for 5 years now and it seems so ours. We know everything about it. We know where the white board is, where the coffee maker is, where my desk is and more importantly who the people inside it are. We feel so comfortable in this place that we don’t think twice about entering it. When we are not in the office, we miss it. We think of returning to it over and over again even if it a lot of times pains us when things don’t work. When there is too much noise and when whatever we try, we can’t fix issues with it. When we are disappointed with everything that there is. When we give up and hope things will be better tomorrow.

But it’s not always the bad things, there have been moments where I have enjoyed a lot. The joy of returning after a vacation, the joy of seeing familiar things. But you get the idea.

Now we are moving…. We have to. .. some of us have moved on. But I am still here ..waiting for some call from someone telling me to move on. I don’t know if I am ready or not. But I guess this has to happen. I just hope its all ok on the other side….

Deep Slumber

Disclaimer: This post is a forced post which my inner self has forced me to undertake because of the deep slumber that I apparently I am in (although I won't think if it in that way ..it's the time taken to ..how do you say it..ya..get inspired)

This post comes after a gap of like 2 months. Well in reality, a lot more than that (as the previous post was ready a long time back..was just lazy to press publish button). The thing is that I have been thinking about it for a long time and ya it's not that I don't have the time..But I just don't have the time...confused? join the group. I am too.

Writing a blog shouldn't be tiresome? right? But I guess if you just want to say some random things without any basis or without proper research, it just highlights your ignorance and laziness.

I can't deny that there weren't many interesting topics to rant about : the movie lucy, the pre-registered studies, the Susan Greenfield controversy and a lot more. And indeed there were a lot of interesting discussions on all of these issues (which also sort of dissuaded me from writing on them - "like m going to write better than that??? huh").

Well, it seems that this entry has become a sort of justification for not writing on the blog. Probably, it is. But I think the more important thing is that I write and write something meaningful (for may be a distinct alien in the future to read!!).

The uncertain past : The confessions (p4)

This is still fiction. Resemblance is still coincidence. 

When I breathed in, I was sure I was in heaven. Mostly because I believed I was a faithful follower and I can't be in hell. Also because of the soft music playing in the background. But my worst fears came true when I realised the panic sounds that were becoming more and more prominent. I still felt too far away from the sounds. My body still felt like a petrificus charm was on me. But I was sure I still had a beating heart in me. I could hear it now.

I was now a regular at understanding black outs. I don't know if it was a great thing that I could think. But I guess that would be necessary for the people working to still keep me alive.
I need to confess my excitement of thinking about the idea of out body experience. I wonder if I'll have one. I had the funniest idea. Probably the least I could do to change the mood.

I don't remember being one with a funny attitude. Although I now hope I was more open to ideas and fun things. It's so strange how petty things seem now that I think about the fights that used to drive me insane. I think about them now and assure myself that there was nothing I could have done at that time. But probably I was wrong and I could have changed the things, something to make it work, something to make it better.

I realize I never said "I love you" to a lot of people. I was always so scared and now when I am, you know, like this, I feel I could have used the words more often. What bad could have happened? It always felt like my heart would explode even if I though of saying that. I remember the times I found out how despised I was and how people used to think about me - cold and distant, arrogant and self-absorbed. I died a little inside that day.

Creating a desktop configuration for neuroimaging analysis

Recently, I had to place an order for a work desktop (and of course you all know that I work with neuroimaging data). So, I had to specify the minimum requirements that I needed in the system. Anyone who has done something like this before would understand the complications (and the joy) associated with this. 

There are a number of parameters to choose from especially when you don’t have a very strict restriction of money. This is complicated by the fact that there are no guidelines that tell you how to proceed. Since, I went through this (and had nothing else to do), I decided to write this post about how I went ahead with the specifications.

Note: Following are mere guidelines!!

First of all, you need to ask certain questions.

1.      Type of work: What kind of data processing do you require? Does your work include basic fMRI processing (resting state and task related), structural analysis, DTI analysis or connectivity analysis etc. Certain kind of analysis would require more processing and RAM while others don’t. My work involves basic task related analysis of fMRI data as well as some structural analysis.

2.      Amount of Money: How much money are you allowed to spend? This might sound trivial, however, money is a very big constraint and you would preferably try to reduce the costs (I will give both high end as well as less expensive options both of which should work fine).

3.      Assembled or not? Do you have the required technical skills to assemble a desktop from basic parts? In most cases, this may not be valid, as most of you would have a purchase/technical store that would get assembled computers from manufactures. Getting an assembled configuration gives you lesser choices but is already optimized by the provider company so that you don’t have to worry about compatibility issues.

So here are my recommendations. I believe it’s always better to get a system better than your current requirements (as they are sort of investments and are not bought frequently). 

The three things that you need to pay the most attention to are : CPU, RAM, Graphics card. 

CPU: There are two major providers of CPU- Intel and AMD. I personally don’t have experience with AMD processors. Intel produces a large variety of CPU processors and there are a number of them to choose. The most famous being the i series processors for laptops and desktops. What you should prefer, however, are the Intel Xeon processors. These are workstation processors designed for stability and continuous work (which I believe most of the neuroimaging folks would relate to!!). Xeon processors are classified according to the series (no surprises there!!). E5 I believe are the latest (as of March 2014). CPU benchmarks (passmark) is a great tool to know how the processor you have chosen performs compared to other processors in the market. You should also check their price performance (compared to price how good they are).

My choices for the CPU:

1.      Intel Xeon E5-1660 v2 @ 3.70GHz

2.      Intel Xeon E5-1650 v2 @ 3.50GHz

3.      Intel Xeon E5-1650 @ 3.20GHz

4.      Intel Core i7-4930K @ 3.40GHz

RAM: RAM is a critical component of the system and you would require lots of it especially for neuroimaging analysis!! Generally, the more the better. A RAM of around 16 GB (preferably divided as 8x2 or better 4x4 ) should work for most of the analysis. Also, it’s important to get the latest and the best in the technology. I would suggest getting DDR3 (third level of RAM technology) at 1866MHz. 

My choice:

1.      16 GB DDR3 1866MHz

Graphics Cards: Many researchers would say that graphics cards are not necessary component of a neuroimaging system.  However, recent advances in image processing and use of heavy visualization softwares requires using atleast a mid level graphics card. It’s important to note that while many of us would be tempted to get the best graphics card from GeForce or Tegra or Tesla (mostly so that the system can satiate our gaming needs as well!!) , Quadro are the preferred graphics cards for neuroimaging analysis. These are designed to be workstation graphics cards and are stable and can work continuously for hours.

My choices:

1.      NVIDIA® Quadro® K2000 2GB GDDR5 CUDA core

2.      NVIDIA® Quadro® 2000D

3.      NVIDIA^® Quadro^® 600, 1 GB, 96 CUDA cores,

There are other requirements that are not so critical like hard disk, operating system, monitor. But they depend more on your preference. I would recommend 2 mechanical Hard disk 1TB or 2TB each (SSDs are new, not so stable, have had issues with Linux!!). I personally prefer Ubuntu 12.04 (Long term support) and  a high resolution 23 inch (1920x1080) monitor.

I took considerable help from these additional resources:

1.      http://www.reddit.com/r/neuro/comments/1f94nu/building_a_pc_for_neuroimaging_data_analysis/

2.      https://sites.google.com/site/mritutorial/iii-neuroimaging-workstation-tutorials/tutorial-1-hardware-recommendations (has suggestions for dell based systems and other suggestions)

3.      http://www.youtube.com/watch?v=LV3YBhrD_D4

4.      http://www.newegg.com/

5.      http://cpuboss.com/

6.      www.nvidia.com/content/quadro_fx_product.../TB-04631-001_v04.pdf

Rejections and applying

I think its one of those times that the emotion component takes the better of you and you just find yourself wondering why, why does it feel bad? You know all the logic in the world says something else. You can defend others' actions, understand why did they do what they did. You clearly understand why you feel what you feel but you can't just help it. You feel something just because you feel it - your mind seems to have renounced all reason and become a slave of your emotions.

You know that it just doesn't matter! It is never going to affect you but just because you expected it to happen, you feel bad about it. And you start questioning everything in the world, think of everything in the most negative way.

Why should it matter?

Well by now you must be wondering why this rant today?? Well, I have been applying for a PhD position and as any student who has ever applied for such things (except for some lucky ****) would tell you, rejection is way of life and totally inevitable. What this leaves you with is momentary highs and lows, some cases of incredible joy (wow this guy replied!!!) and other points of depression (I am totally not worth. what am I even doing?? Right choice of career???), but mostly depression.

I think it's a excruciating experience but it is something that people have to go through. No matter how sugar coated the rejection might be "I believe that you are an exceptional candidate with your extensive research experience", "Your CV looks very impressive", "We were all extremely impressed by your application", "I have confidence that you will find a PhD position where your skills will be an outstanding asset.", "I wish you all the success in future studies", it still a rejection and you are left with daunting task of starting all over again and look for other opportunities (Not that I suggest that language of these should change to "Your CV sucks", "I don't think you'll be able to get any position"). It's just that it feels bad and you don't need to be in this field to agree that rejection does hurt especially if you have worked hard for it. Unfortunately, all you can do is sulk, take a deep breath and write a blog about it.....

Few things people do to their research papers (which they should not..)

Writing a research paper is difficult, very difficult. I found it out the hard way when I had to write my first research paper. Reading a paper is very easy but writing something that you have done (without copying and pasting from similar papers (BTW also called plagiarism)) is very difficult and you have to be very innovative but at the same time sound technical, clear and interesting. After I actually wrote the paper (which took me and my colleague around 6 months), the way I look at the papers completely changed. Now, when I see certain portions of the published peer reviewed papers, I know that this section was completely due to the pressure of the reviewers, this section was because the authors wanted to highlight certain aspects (and hide some others). So, now you would be thinking, why have I started this rant of mine? Good question! It is because there are certain things that have really annoyed me about the papers which might be inherent problems of the field. But still annoying. Specifically, I am upset about some of the practices people do and the way they write their methods section.

      1.       Talaraich Co-ordinates. I do respect the idea and effort that was  put in making the Talaraich atlas. But, now I believe if you really want to confuse people and don’t want your study to be replicated, you use these co-ordinates. I know that there would be people who would disagree with me, but I guess this is my opinion. First, there are well known issues with the Talaraich atlas (from a single subject etc.). A lot has been written about it, so I won’t elaborate here. Second of all, there is no single accepted way of transforming it into MNI. There are ways - Matthew Brett’s script and lot of others (see http://www.sdmproject.com/utilities/?show=Coordinates). But mostly they are empirical and approximations. So, now I just get annoyed when I see Talaraich coordinates.

      2.       Cluster level correction: The field is well aware of the issues of multiple comparison and a lot has been said – some in a funny way and some in more serious ways. However, the issues has now taken a different direction and incorrect or less understood ways of correction have come up. One of them being the Alphasim/ monte carlo simulation method which is often poorly described/incorrectly used in the studies (see Bennett, Wolford, & Miller, 2009). I am not saying that the method is wrong. But the way it is written is often unclear (probably even to the authors). This leads to misleading statements like ‘The results are corrected for multiple comparisons’ in the papers when they are corrected at cluster level and not on the voxel level. Also, FDR voxel level has been proven not to be appropriate for inference on peaks or regions of activation than the cluster level FDR (Chumbley & Friston, 2009). SPM software has already stopped showing results at FDR voxel level. However, FDR voxel level are still prevalent in the papers.

      3.       Results on Brain slices. I know that a lot of people will disagree with me and say that the way of presenting your fmri results is upto you. But I would argue that if you really like your results on brain slices, put them in supplementary or next to a whole brain image. What brain slices do, is that they let u see only what the authors want you to see which I believe is against the idea of a results section. The results section should have all the results as it is without the interference from the authors – their way of thinking or their beliefs. I know that this might be difficult to take out from the paper, but we can try with results that just don’t show one slice of brain! So now, whenever I see fmri results on a brain slice, I start believing that there were probably some activations, that the authors didn’t want me to see and more often than not, when I see the results table, there are other regions which are activated. Lot of times hiding other activations might not be the aim of the authors but to showcase specifically the activations, however, often what this leads to is a bias in the mind of readers (quite frankly how many of us go through the tables for list of areas activated in each task unless we are looking for co-ordinates or specific regions). The reason I stress on this is because, what this eventually leads to is strong ideas in the field about the task and if the paper is influential enough, to studies that tend to approve the regions in the studies forming a vicious circle questioning studies that show other regions activated in similar tasks.

      4.       Short methods sections. This is very true of some journals that simply think that methods are not so important, it’s the results that are critical. I believe that methods are almost as important as the methods. For example, there are multiple ways to make a something that looks like a cake, but all of them might not be edible. 

      5.       Previously used methods: The sure shot way to ensure that your results are never replicated ever – “The protocol previously used in the papers (1 2 also see 3 ) was used for the data”. Most often the papers 1,2 as well as 3 refer to different protocols which are somewhat related to the current paper but possibly use completely different parameters (which is not very obvious). A reader only interested in the fascinating results might not really bother about them but people who would like to replicate the experiment would be sent on a treasure hunt to find what parameters were actually used. Strangely, the journals do not mind such statements.

      6.       Methods in books. This is another way to ensure experiments are not replicated. “The values were calculated using the criteria X (reference to a book)” Often this book is a textbook, not freely available and even if u manage to get your hands on it, you are on another journey to hunt the location of the criteria in the book.

The reporting of methods is improving however, with efforts like pre-registration of studies and other practices of reporting results. Hopefully, this will improve further in future.

Italian Survival Guide

Three months ago, I was thrown into the Italian world when I joined the lab there. The experience has been awesome, stupendous. I have been blown away by the beauty of Italy. Let me tell you that there is a lot of difference between the photos that you see on the internet and the actual places. The pics are, I think, one dimensional.
However, I am not going to talk about something that a lot of people have already talked about and a lot better than what I possibly can. I am about to write about the not so great aspect of coming to Italy for people who don't know Italian. As you already know, I am an Indian and so have absolutely no idea of Italian language. It was difficult for me and even though I did start practicing the language like 2 months before arriving, I felt it was not enough. There were certain things that I wished I knew before coming that would have really helped me a lot. However, I believe these things might help you. What I am going to write down are certain sentences/phrases that will help you in the initial period here. This is in no way a substitution for learning Italian and certainly no excuse for not learning the language. I strongly urge you to learn it once you are here. I will also provide you a list of places in Genoa where you can learn Italian. Ok, so let's start.

I will start with some distinctions between English and Italian and some suggestions which probably help understand what to use and importantly what not to!!

1. What is important to know is that even though English does not have distinction between formal and informal words, it is widely prevalent  in Italian (and other languages). So, it might sound rude if you talk in an informal way to a stranger elder to you. (although i have never found Italians to be angry if you use the language improperly but instead they offer you help).

2. The construction of sentences is very similar to English and a lot of the words are actually very similar to English. Probably -  probabilmente. type - tipo. case - caso. Of course, the pronunciation is different.

3. While learning Italian, don't think you are learning English and translate it directly (although it's unavoidable) but try and understand that the way some things are said (and thought) in Italian are not the same as in English. For example, although the literal translation of "what is your name?" in Italian would be "qual è il tuo nome", this is not the way it is said in Italian. Instead, "come ti chiami" is used which literaly translated to English would be "How do you call yourself?. So the point is that don't memorize that what's your name in Italian is "come ti chiami" but instead realize that things are thought differently in Italian and acknowledge it.

4. You will find that although in English, you would always need a pronoun, it's optional and almost never used in spoken Italian. The reason for that is that unlike in English, the verb in Italian changes form according to the person it refers to. For example, the verb in the infinite form for 'ear' is mangiare, this takes the form 'mangio' if you are talking about yourself, 'mangi' if you are talking to second person and 'mangia' if you are talking about a third person. so just saying the word 'mangio' is equivalent to saying 'io mangio' - I eat.

5. Gender- Unlike English, Italian (and many other languages) assigns gender to inanimate objects as well. This might sound a bit odd to native English speakers, but this is important in Italian and may be a bit difficult to comprehend. Although, you may not worry about the gender if all you want is a brief knowledge of Italian (people will understand if you do a mistake with gender but still may be able to understand more or less what you mean) . For example, a ticket has a masculine gender - 'biglietto'. Generally speaking, words that have 'o' in the ending are masculine and ending in 'a' are feminine. Correspondingly, the plurals of these words end in 'i' and 'e'. Just be careful of one more thing, some words that have 'e' in the ending may also be singular masculine or singular feminine. So, be cautious while applying the reverse logic of 'e' to plural feminine.

6. Articles- Although, the articles are not so often used (or skipped sometimes) in English, they are very important in Italian. What does complicate the case in Italian is that the article changes according to the gender and the number. The basic articles being - un (a), il (the) for masculine and una (a) and la (the) for feminine words. Since, this is not supposed to be an extensive review of Italian, I will (and have skipped) skip a lot of complications. There are lot of variations in the articles as well.

7. The distinction between declarative sentences and interrogative sentences is not very clear in Italian as it is in English (also because the pronoun is usually skipped). What I mean by that is that in English the sentences : I can have an apple (declarative) and Can I have an apple? (interrogative)  are clearly distinguishable because of the order of pronoun. However, in Italian the same sentences would be: Posso avere una mela (I can have an apple). Posso avere una mela? (Can I have an apple?).

Basic words/phrases (of course every learn Italian video or book or course has it). What I will provide is explanation of when to use them:

1. Ciao - Hello and Bye. Use with care. This is an informal way of saying Hi. So, probably won't look nice if talking to an older officer or a complete stranger a lot elder to you (or alternatively if you use a very formal way to talk to a young kid, it might sound very funny to the Italians).

2. Buon giorno - Good day. This is a very useful word. This is sort of the safe word that I have been using for some time. It can be used in place of Ciao to almost anyone - young and adult. This is also the word people usually use when one enters a shop. It is polite to great people and you will find it prevalent everywhere.

3. Buona sera - Good Evening. The substitute for Buon giorno. in the evening. Same usage as buon giorno.

4. Posso avere un biglietto?: Can I have a ticket? I am not sure if this applies to other places in Italy, but in Genova, the tickets for local buses (and train within city limits) are purchased from newspaper/tobacco shops. If you would like to travel somewhere via a bus or other means you can use this statement for asking for a ticket.

5. Grazie/Grazie mille: Thanks./ thanks a ton!!

A possible scenario: Buying a ticket

You: Buon giorno/ Buona sera
Vendor: Buon giorno/ Buona sera (Alternatively: Dimmi - tell me)
You - Posso avere un  biglietto di A.M.T. , ordinario? (Alternatively : Posso comprare(buy) un  biglietto? in genova AMT is the main agency for tickets and ordinario is the ticket type).
Vendor - Si
(gives the ticket)
Vendor - uno e sessanta (1.60 euros)
You - (giving money)  Grazie
Vendor : Grazie, Ciao. (Alt Arrivederci - Good bye!)
You : Ciao/ Arrivederci

In a supermarket while billing:

Supermarket employee: hai tessera? (do you have a card? - like a loyalty card)
You: No.
Supermarket employee:: sacchetto? (a plastic carry bag?)
You : No.

Misc. :

Dov'è il bagno? Where is the bathroom/ toilet?

Permesso: Asking for permission to go through. This is used when there is someone blocking the way and you would like to go through. 

scusa/scusi : Sorry (formal/informal). use Scusi in formal situations. these words are used in cases where you are in a hurry and you accidentally hit someone.  

Vorrei: I would like to. For example : vorrei una pizza (I would like a pizza) .

non parlo Italiano: I don't speak Italian.

okay: ok
va bene: Alright.

Quant'e' : How much? ( after purchasing a meal at a restaurant )


Some of the resources that I find useful:
1. Duolingo : a very nice app for learning different languages.
2. italian-verbs.com: a list of a lot of Italian verbs and different forms according to person and tense.

Some of the useful videos :
1. This is one of the most useful resource I found, it gives a good ideal of Italian: http://www.youtube.com/playlist?list=PLKICLEvD2DfpUtjb4nc0Vr9QfdYn_Ursj


I will keep adding more in the due course!!