PEARL — It’s been a rough three weeks for Southern Miss.

Once firmly in command atop the Conference USA standings and in contention for a national seed in the NCAA Tournament, the Golden Eagles watched it all slip away. A three-game lead disintegrated. A shot at the Conference USA tournament championship fell apart with a loss in extra innings and a flat offensive performance in the finale.

The good news is, the Golden Eagles are firmly entrenched in the NCAA Tournament’s field of 64, which will be announced today. But just like last season, the Golden Eagles will have to start on the road, where they are 12-8 and 3-2 at neutral sites.

The question is where.

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NCAA Tourney regional sites

Atlanta, Ga.

Georgia Tech

Austin, Texas

Texas

Fullerton, Calif.

Cal State Fullerton

Chapel Hill, N.C.

North Carolina

Charlottesville, Va.

Virgina

Clemson, S.C.

Clemson

College Station, Texas

Texas A&M

Columbia, S.C.

South Carolina

Corvallis, Ore.

Oregon State

Fort Worth, Texas

TCU

Gainesville, Fla. 

Florida

Houston, Texas

Rice

Los Angeles, Calif.

UCLA

Nashville, Tenn.

Vanderbilt

Tallahassee, Fla.

Florida State

Tempe, Ariz.

Arizona State

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“Those things are out of our control. The only thing that was in our control was to come out and win this game and we didn’t do it,” Southern Miss coach Scott Berry said after Friday night’s 4-0 loss to East Carolina in the C-USA Tournament finale. “We knew the stakes going in.”

As for Mississippi State, the Bulldogs (34-23) bowed out of the SEC Tournament with a 7-2 loss to Arkansas Thursday and finished 0-2. With a 27th ranking in the Rankings Percentage Index, Mississippi State coach John Cohen likes his team’s odds to make the field for the first time since 2007.

“I like our chances,” Cohen said in a team release. “We have played well enough this year to deserve a spot. I feel like if our kids get in a tournament, we have a chance to win some games. We have a chance to win a regional.”

Southern Miss (39-17) likely would have locked up a regional if it had fared better against Houston. The Cougars took two out of three from USM in a series in Houston on May 13-15, then won in 14 innings in the C-USA Tournament on Thursday night. Three of their four meetings were decided by one run, and Thursday’s loss cost USM a spot in the tournament championship game against Rice — a highly-ranked opponent that could have further bolstered the Golden Eagles’ regional chances.

Southern Miss then managed only three hits against East Carolina ace Seth Maness in Friday night’s tournament finale. That capped a nine-game stretch to end the season in which USM won only three games.

“The last couple of weeks have been really tough on us, but that’s baseball. It happens to everybody,“ USM outfielder Kameron Brunty said. “We’re going to get back on track. We have to clear our minds out and get these bad three weeks out of the way. Get right back into practice on Monday. I think after two days off everybody will be ready to go.”

Wherever they end up, the Golden Eagles have plenty of personnel issues to deal with. Two starting pitchers, Geoffrey Thomas and Jonathan Thompson, were declared academically ineligible last week and missed the C-USA Tournament. Thomas could return this week, but Thompson is out for the season.

Southern Miss did get a couple of solid performances from freshman Boomer Scarborough and junior Josh Thomason in the conference tournament, but the lack of overall pitching depth could be a problem moving forward.

There’s also concern on the hitting side. Tyler Koelling, the Ferriss Trophy winner, did not play in the conference tournament because of a hamstring injury. First baseman Adam Doleac skipped the game against East Carolina because of a foot injury. The status of both players for the regional is uncertain.

“When somebody goes down, somebody else gets an opportunity. That’s the way you have to look at it. You hope they’re ready for the opportunity and willing to get out there. There will be opportunities next week,” Berry said