Since his 1999 debut “Anyon Kimuchi (Annyong Kimchi),” a documentary about his zainichi (ethnic Korean) family, Tetsuaki Matsue has been interested in those on the margins of Japanese society — though he is hardly the director-as-crusader.

Instead, as he showed in “Raibu Tepu (Live Tape),” winner of the Best Film prize in the Japanese Eyes section at the 2009 Tokyo International Film Festival, he can be something of a coconspirator and confessor. Following Bob Dylan-esque singer-songwriter Kenta Maeno as he busked through the crowded streets of Tokyo’s Kichijoji neighborhood, Matsue conducted a running dialogue with his subject on his work and life that began as drolly funny but became surprisingly moving, as Maeno revealed his conflicted feelings toward his father and his doubts about the future.

The subject of Matsue’s new “Furasshubakku Memorizu 3D (Flashback Memories 3D),” however, was “totally different (from Maeno),” Matsue says in an interview at the office of production company Space Shower Networks. Hiroki Morimoto, a didgeridoo player better known as Goma whose struggle with memory loss is the film’s focus, “sees the world from a different place,” Matsue explains. “He exists on a totally different plane from me.”

When Matsue first saw Goma perform, at a comeback concert shortly after the March 11, 2011 earthquake, he said he initially had an image of him “as someone with a disability — and I had no desire to make a film from that approach.” But when Matsue heard him play the didgeridoo, a traditional wind instrument of the Australian Aborigines, he felt what he described as a “tremendous energy.” “He may have had a disability,” Matsue adds, “but I saw him as a musician.”

Also, the timing of his encounter with Goma, Matsue notes, was just right. “It was just after 3/11, when everyone was feeling kind of gloomy about where Japan was headed,” he says. “But when I met Goma I felt revitalized — he was such a positive person.”

Inspired by Goma’s music and personality, Matsue wanted “to film his brain — that is, what he was feeling, the world he was seeing.” While admitting that Goma’s memory dysfunction is a “misfortune,” Matsue adds that Goma was “not playing music to spread that misfortune. Instead he was generating good energy — and I wanted to express that.” The use of 3-D “hit me as the way to do it,” says Matsue.

This sort of tailoring of method to theme, he adds, is “my way of filming; I believe there has to be a link between the two.”

“For example, I made ‘Live Tape’ with one cut, but I’m not going to make another film with one cut,” he explains. “This time as well, I decided from the beginning that I wanted to film in 3-D. When I heard Goma’s music, inside my head I was already thinking ‘3-D.’ “

Also, rather than sit down with Goma and his wife for the standard on-screen interviews, Matsue decided to film the journals the couple had written as Goma recovered from the car accident that had caused his memory loss.

“There was so much energy in those journals,” he explains. “They had both written some extraordinary things, things I knew I couldn’t get them to express just by asking them questions in an interview. I thought the words Goma had handwritten had more power.”

The audience at the 2012 Tokyo International Film Festival, where “Flashback Memories 3D” had its world premiere, evidently agreed, voting the film its favorite in the competition. Also, the film has been lavishly praised by foreign reviewers and invited to festivals abroad, beginning with the Cinemanila International Film Festival in the Philippines in December. This is not a first for Matsue: “Live Tape” and other films of his also screened widely on the festival circuit — and he has spotted no great difference between audiences in Japan and elsewhere.

“They tend to be young and interested in subcultures rather than mainstream culture,” he observes. “They want information and get it from iPhones. When I ask them what sort of movies they find interesting, they mention ones made by (Takashi) Miike and (Sion) Sono; it’s the same everywhere. It’s easier now to connect to those types of people, so the potential for independent films is going to grow.”