1

I am currently studying masters in the US and I hold a J1 visa.

I want to continue my PhD in a Canadian university can I apply for a Canadian student visa (assuming I have been accepted by Canadian University) or must I obtain the visa from my country of permanent residence?

3

I found this on the official website of Citizenship and Immigration Canada

You must select the visa office that serves your country of nationality or the country where you have been legally admitted for at least one year.

I would think that a J1 visa could be enough to satisfy this requirement but I am not sure.

Additionally, for temporary residence or study permits, you can apparently apply in any Visa Application Centre and your application will then be forwarded to the relevant visa office. If I understand this correctly (I never did it myself), you cannot choose which visa office will handle your application but you won't necessarily need to go to this office in person.

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